rs4301994

Variant names:

• chr15-96823885-T-C
• rs4301994

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0596 in 152,224 control chromosomes in the GnomAD database, including 382 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 0.060 (382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.946
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

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: 0.0595 AC: 9056 AN: 152106 Hom.: 380 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0640

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0596 AC: 9074 AN: 152224 Hom.: 382 Cov.: 31 AF XY: 0.0582 AC XY: 4332 AN XY: 74436

African (AFR) AF: 0.105 AC: 4357 AN: 41554

American (AMR) AF: 0.0381 AC: 582 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0498 AC: 173 AN: 3472

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5184

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4828

European-Finnish (FIN) AF: 0.0476 AC: 505 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0444 AC: 3021 AN: 67992

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

Alfa AF: 0.0482 Hom.: 282

Bravo AF: 0.0617

Asia WGS AF: 0.0290 AC: 99 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.65
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs4301994; hg19: chr15-97367115;