rs2616521

Variant names:

• chr3-5013893-T-C
• rs2616521

Your query was ambiguous. Multiple possible variants found:

• chr3-5013893-T-C
• chr3-5013893-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.873 in 151,994 control chromosomes in the GnomAD database, including 58,242 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 0.87 (58242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 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: 0.873 AC: 132622 AN: 151876 Hom.: 58199 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.873 AC: 132721 AN: 151994 Hom.: 58242 Cov.: 31 AF XY: 0.869 AC XY: 64576 AN XY: 74280

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.893

Alfa AF: 0.907 Hom.: 21318

Bravo AF: 0.866

Asia WGS AF: 0.800 AC: 2783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2616521; hg19: chr3-5055578;