5-154457546-C-T

Variant names:

• chr5-154457546-C-T
• rs148763909
• NM_024632.6:c.*1518C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_024632.6(SAP30L):​c.*1518C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,244 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.020 (43 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SAP30L NM_024632.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 15 publications found

Genes affected

SAP30L (HGNC:25663): (SAP30 like) Enables several functions, including non-sequence-specific DNA binding activity, bending; phosphatidylinositol phosphate binding activity; and zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0197 (2993/152244) while in subpopulation SAS AF = 0.0429 (207/4822). AF 95% confidence interval is 0.0381. There are 43 homozygotes in GnomAd4. There are 1442 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 43 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024632.6. 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
	SAP30L	NM_024632.6	MANE Select	c.*1518C>T		3_prime_UTR	Exon 4 of 4	NP_078908.1	Q9HAJ7-1
	SAP30L	NM_001131062.2		c.*1518C>T		3_prime_UTR	Exon 3 of 3	NP_001124534.1	Q9HAJ7-3
	SAP30L	NM_001131063.2		c.*1518C>T		3_prime_UTR	Exon 3 of 3	NP_001124535.1	Q9HAJ7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAP30L	ENST00000297109.11	TSL:1 MANE Select	c.*1518C>T		3_prime_UTR	Exon 4 of 4	ENSP00000297109.5	Q9HAJ7-1

Frequencies

GnomAD3 genomes AF: 0.0197 AC: 2997 AN: 152126 Hom.: 43 Cov.: 33

Gnomad AFR AF: 0.00555

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.00860

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0220

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0197 AC: 2993 AN: 152244 Hom.: 43 Cov.: 33 AF XY: 0.0194 AC XY: 1442 AN XY: 74430

African (AFR) AF: 0.00553 AC: 230 AN: 41558

American (AMR) AF: 0.0262 AC: 400 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4822

European-Finnish (FIN) AF: 0.00860 AC: 91 AN: 10586

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0284 AC: 1932 AN: 68014

Other (OTH) AF: 0.0218 AC: 46 AN: 2114

Alfa AF: 0.0228 Hom.: 80

Bravo AF: 0.0190

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.090
DANN	Benign	0.76
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs148763909; hg19: chr5-153837106;