rs1012709

Variant names:

• chr7-131742467-A-C
• rs1012709

Your query was ambiguous. Multiple possible variants found:

• chr7-131742467-A-C
• chr7-131742467-A-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 0.147 in 152,220 control chromosomes in the GnomAD database, including 4,688 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 0.15 (4688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.147 AC: 22298 AN: 152102 Hom.: 4673 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.00922

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00594

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.147 AC: 22348 AN: 152220 Hom.: 4688 Cov.: 32 AF XY: 0.143 AC XY: 10680 AN XY: 74442

African (AFR) AF: 0.459 AC: 19037 AN: 41476

American (AMR) AF: 0.0570 AC: 872 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5182

South Asian (SAS) AF: 0.0446 AC: 215 AN: 4826

European-Finnish (FIN) AF: 0.00922 AC: 98 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00594 AC: 404 AN: 68026

Other (OTH) AF: 0.116 AC: 245 AN: 2112

Alfa AF: 0.0426 Hom.: 174

Bravo AF: 0.166

Asia WGS AF: 0.172 AC: 599 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	0.70
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1012709; hg19: chr7-131427226;