chr17-1406953-A-G

Variant names:

• chr17-1406953-A-G
• rs7213811

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 0.584 in 151,798 control chromosomes in the GnomAD database, including 26,276 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 0.58 (26276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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: 0.584 AC: 88627 AN: 151680 Hom.: 26249 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.584 AC: 88710 AN: 151798 Hom.: 26276 Cov.: 32 AF XY: 0.580 AC XY: 43011 AN XY: 74162

African (AFR) AF: 0.665 AC: 27512 AN: 41360

American (AMR) AF: 0.636 AC: 9700 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1911 AN: 3464

East Asian (EAS) AF: 0.335 AC: 1726 AN: 5154

South Asian (SAS) AF: 0.604 AC: 2909 AN: 4818

European-Finnish (FIN) AF: 0.493 AC: 5200 AN: 10538

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37825 AN: 67906

Other (OTH) AF: 0.585 AC: 1233 AN: 2108

Alfa AF: 0.576 Hom.: 3004

Bravo AF: 0.592

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.34
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs7213811; hg19: chr17-1310247;