rs2601773

Variant names:

• chr16-3951897-C-A
• rs2601773

Your query was ambiguous. Multiple possible variants found:

• chr16-3951897-C-A
• chr16-3951897-C-T

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 0.414 in 151,930 control chromosomes in the GnomAD database, including 13,736 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 0.41 (13736 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.414 AC: 62880 AN: 151812 Hom.: 13732 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.414 AC: 62910 AN: 151930 Hom.: 13736 Cov.: 31 AF XY: 0.411 AC XY: 30539 AN XY: 74274

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.409

Alfa AF: 0.465 Hom.: 22673

Bravo AF: 0.406

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2601773; hg19: chr16-4001898;