rs1657290

Variant names:

• chr7-155166994-C-T
• rs1657290

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 0.498 in 152,134 control chromosomes in the GnomAD database, including 19,198 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 0.50 (19198 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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: 0.498 AC: 75740 AN: 152016 Hom.: 19184 Cov.: 34

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.498 AC: 75791 AN: 152134 Hom.: 19198 Cov.: 34 AF XY: 0.501 AC XY: 37232 AN XY: 74362

African (AFR) AF: 0.546 AC: 22650 AN: 41502

American (AMR) AF: 0.445 AC: 6807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3666 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2463 AN: 4824

European-Finnish (FIN) AF: 0.479 AC: 5062 AN: 10570

Middle Eastern (MID) AF: 0.503 AC: 145 AN: 288

European-Non Finnish (NFE) AF: 0.464 AC: 31548 AN: 67998

Other (OTH) AF: 0.509 AC: 1075 AN: 2110

Alfa AF: 0.475 Hom.: 10695

Bravo AF: 0.496

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1657290; hg19: chr7-154958704; COSMIC: COSV60313268;