rs10406920

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000598188.6(BABAM1):​c.787-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,608,172 control chromosomes in the GnomAD database, including 25,508 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2410 hom., cov: 32)
Exomes 𝑓: 0.17 ( 23098 hom. )

Consequence

BABAM1
ENST00000598188.6 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00002312
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.798
Variant links:
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]
USHBP1 (HGNC:24058): (USH1 protein network component harmonin binding protein 1) Enables PDZ domain binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BABAM1NM_014173.4 linkuse as main transcriptc.787-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000598188.6 NP_054892.2
BABAM1NM_001033549.3 linkuse as main transcriptc.787-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant NP_001028721.1
BABAM1NM_001288756.2 linkuse as main transcriptc.787-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant NP_001275685.1
BABAM1NM_001288757.2 linkuse as main transcriptc.562-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant NP_001275686.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BABAM1ENST00000598188.6 linkuse as main transcriptc.787-6C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_014173.4 ENSP00000471605 P1Q9NWV8-1

Frequencies

GnomAD3 genomes
AF:
0.172
AC:
26092
AN:
152062
Hom.:
2411
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.0855
Gnomad AMR
AF:
0.107
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.238
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.187
Gnomad OTH
AF:
0.159
GnomAD3 exomes
AF:
0.147
AC:
35422
AN:
240154
Hom.:
3021
AF XY:
0.150
AC XY:
19548
AN XY:
130652
show subpopulations
Gnomad AFR exome
AF:
0.183
Gnomad AMR exome
AF:
0.0790
Gnomad ASJ exome
AF:
0.161
Gnomad EAS exome
AF:
0.000562
Gnomad SAS exome
AF:
0.114
Gnomad FIN exome
AF:
0.240
Gnomad NFE exome
AF:
0.178
Gnomad OTH exome
AF:
0.150
GnomAD4 exome
AF:
0.173
AC:
252053
AN:
1455992
Hom.:
23098
Cov.:
32
AF XY:
0.172
AC XY:
124619
AN XY:
723778
show subpopulations
Gnomad4 AFR exome
AF:
0.182
Gnomad4 AMR exome
AF:
0.0825
Gnomad4 ASJ exome
AF:
0.172
Gnomad4 EAS exome
AF:
0.000505
Gnomad4 SAS exome
AF:
0.118
Gnomad4 FIN exome
AF:
0.237
Gnomad4 NFE exome
AF:
0.185
Gnomad4 OTH exome
AF:
0.161
GnomAD4 genome
AF:
0.171
AC:
26089
AN:
152180
Hom.:
2410
Cov.:
32
AF XY:
0.170
AC XY:
12611
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.185
Gnomad4 AMR
AF:
0.107
Gnomad4 ASJ
AF:
0.173
Gnomad4 EAS
AF:
0.00154
Gnomad4 SAS
AF:
0.108
Gnomad4 FIN
AF:
0.238
Gnomad4 NFE
AF:
0.187
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.175
Hom.:
1766
Bravo
AF:
0.161
Asia WGS
AF:
0.0570
AC:
202
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
3.4
DANN
Benign
0.38
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000023
dbscSNV1_RF
Benign
0.0020
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10406920; hg19: chr19-17389648; COSMIC: COSV63921267; COSMIC: COSV63921267; API