rs1657290

chr7-155166994-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 0.498 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.509

Alfa AF: 0.475 Hom.: 9745

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

Splicing

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

Publications

LitVar

Other links and lift over

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