chr15-95976212-C-A

Variant names:

• chr15-95976212-C-A
• rs4984472

Variant summary

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

The variant allele was found at a frequency of 0.0183 in 152,176 control chromosomes in the GnomAD database, including 45 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 0.018 (45 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0183 (2791/152176) while in subpopulation AFR AF = 0.0374 (1552/41506). AF 95% confidence interval is 0.0358. There are 45 homozygotes in GnomAd4. There are 1323 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2779 AN: 152058 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0235

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0183 AC: 2791 AN: 152176 Hom.: 45 Cov.: 32 AF XY: 0.0178 AC XY: 1323 AN XY: 74414

African (AFR) AF: 0.0374 AC: 1552 AN: 41506

American (AMR) AF: 0.0113 AC: 173 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3470

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5160

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4818

European-Finnish (FIN) AF: 0.00132 AC: 14 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0121 AC: 820 AN: 68012

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

Alfa AF: 0.00109 Hom.: 0

Bravo AF: 0.0193

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0080
DANN	Benign	0.74
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs4984472; hg19: chr15-96519441;