rs2641915

Variant names:

• chr16-18765880-T-C
• rs2641915

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.556 in 136,260 control chromosomes in the GnomAD database, including 22,097 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 0.56 (22097 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS2: High Homozygotes in GnomAd4 at 22097 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: 0.556 AC: 75657 AN: 136178 Hom.: 22066 Cov.: 22

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.556 AC: 75729 AN: 136260 Hom.: 22097 Cov.: 22 AF XY: 0.546 AC XY: 35729 AN XY: 65496

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.700 AC: 24962 AN: 35680

American (AMR) AF: 0.512 AC: 6822 AN: 13326

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2096 AN: 3230

East Asian (EAS) AF: 0.219 AC: 1096 AN: 4996

South Asian (SAS) AF: 0.435 AC: 1851 AN: 4260

European-Finnish (FIN) AF: 0.473 AC: 4283 AN: 9046

Middle Eastern (MID) AF: 0.591 AC: 162 AN: 274

European-Non Finnish (NFE) AF: 0.525 AC: 32987 AN: 62806

Other (OTH) AF: 0.547 AC: 984 AN: 1800

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.566 Hom.: 2990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.84
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2641915; hg19: chr16-18777202;