ENST00000602066.5:c.-58C>T

Variant names:

• chr19-17268749-C-T
• rs10424178
• ENST00000602066.5:c.-58C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000602066.5(BABAM1):​c.-58C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,507,020 control chromosomes in the GnomAD database, including 30,499 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.22 (4474 hom., cov: 31)
  • Exomes 𝑓: 0.19 (26025 hom.)
• Consequence: BABAM1 ENST00000602066.5 5_prime_UTR
• Scores: Splicing: ADA: 0.00003828
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.322
• Publications: 17 publications found

Genes affected

BABAM1 (HGNC:25008): (BRISC and BRCA1 A complex member 1) Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; positive regulation of DNA repair; and protein K63-linked deubiquitination. Located in cytosol and nuclear body. Part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000269307 (HGNC:):

USHBP1 (HGNC:24058): (USH1 protein network component harmonin binding protein 1) Enables PDZ domain binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 19-17268749-C-T is Benign according to our data. Variant chr19-17268749-C-T is described in ClinVar as Benign. ClinVar VariationId is 1227766.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602066.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM1	NM_014173.4	MANE Select	c.-13-45C>T		intron	N/A	NP_054892.2	Q9NWV8-1
	BABAM1	NM_001033549.3		c.-51-7C>T		splice_region intron	N/A	NP_001028721.1	Q9NWV8-1
	BABAM1	NM_001288756.2		c.-13-45C>T		intron	N/A	NP_001275685.1	Q9NWV8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM1	ENST00000602066.5	TSL:1	c.-58C>T		5_prime_UTR	Exon 1 of 6	ENSP00000471246.1	M0R0I0
	BABAM1	ENST00000598188.6	TSL:1 MANE Select	c.-13-45C>T		intron	N/A	ENSP00000471605.1	Q9NWV8-1
	BABAM1	ENST00000359435.8	TSL:1	c.-51-7C>T		splice_region intron	N/A	ENSP00000352408.3	Q9NWV8-1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34161 AN: 151836 Hom.: 4469 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.200

GnomAD2 exomes AF: 0.165 AC: 24626 AN: 148944 AF XY: 0.164

Gnomad AFR exome AF: 0.353

Gnomad AMR exome AF: 0.0925

Gnomad ASJ exome AF: 0.177

Gnomad EAS exome AF: 0.000434

Gnomad FIN exome AF: 0.242

Gnomad NFE exome AF: 0.192

Gnomad OTH exome AF: 0.159

GnomAD4 exome AF: 0.190 AC: 257692 AN: 1355066 Hom.: 26025 Cov.: 30 AF XY: 0.188 AC XY: 124862 AN XY: 663854

African (AFR) AF: 0.356 AC: 10817 AN: 30422

American (AMR) AF: 0.0994 AC: 3026 AN: 30446

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 3848 AN: 20764

East Asian (EAS) AF: 0.000530 AC: 20 AN: 37752

South Asian (SAS) AF: 0.121 AC: 8646 AN: 71400

European-Finnish (FIN) AF: 0.240 AC: 9961 AN: 41504

Middle Eastern (MID) AF: 0.130 AC: 654 AN: 5048

European-Non Finnish (NFE) AF: 0.198 AC: 210375 AN: 1061688

Other (OTH) AF: 0.185 AC: 10345 AN: 56042

GnomAD4 genome AF: 0.225 AC: 34187 AN: 151954 Hom.: 4474 Cov.: 31 AF XY: 0.221 AC XY: 16388 AN XY: 74274

African (AFR) AF: 0.345 AC: 14278 AN: 41412

American (AMR) AF: 0.138 AC: 2109 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.111 AC: 537 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2527 AN: 10534

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13540 AN: 67956

Other (OTH) AF: 0.197 AC: 416 AN: 2110

Alfa AF: 0.196 Hom.: 2597

Bravo AF: 0.222

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		-0.32
PromoterAI		-0.012	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000038
dbscSNV1_RF	Benign	0.13
SpliceAI score (max)		0.25		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.25		Position offset: 7

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10424178;

hg19: chr19-17379558;