rs1708403

Variant names:

• chr7-134467612-G-A
• rs1708403

Your query was ambiguous. Multiple possible variants found:

• chr7-134467612-G-A
• chr7-134467612-G-C
• chr7-134467612-G-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 0.571 in 151,786 control chromosomes in the GnomAD database, including 25,894 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 0.57 (25894 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.571 AC: 86632 AN: 151668 Hom.: 25855 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.571 AC: 86723 AN: 151786 Hom.: 25894 Cov.: 31 AF XY: 0.564 AC XY: 41857 AN XY: 74182

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.545

Alfa AF: 0.381 Hom.: 863

Bravo AF: 0.586

Asia WGS AF: 0.534 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708403; hg19: chr7-134152364;