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. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.271 AC: 11223 AN: 41420

American (AMR) AF: 0.412 AC: 6280 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2148 AN: 5148

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4820

European-Finnish (FIN) AF: 0.455 AC: 4799 AN: 10552

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33522 AN: 67958

Other (OTH) AF: 0.409 AC: 865 AN: 2114

Alfa AF: 0.460 Hom.: 28265

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2601773; hg19: chr16-4001898;