rs2909679

Variant names:

• chr7-131649853-T-C
• rs2909679

Your query was ambiguous. Multiple possible variants found:

• chr7-131649853-T-C
• chr7-131649853-T-G

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 0.25 in 152,158 control chromosomes in the GnomAD database, including 10,339 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 0.25 (10339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37955 AN: 152040 Hom.: 10291 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.250 AC: 38070 AN: 152158 Hom.: 10339 Cov.: 32 AF XY: 0.246 AC XY: 18302 AN XY: 74398

African (AFR) AF: 0.675 AC: 28010 AN: 41476

American (AMR) AF: 0.154 AC: 2361 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1801 AN: 5158

South Asian (SAS) AF: 0.183 AC: 884 AN: 4828

European-Finnish (FIN) AF: 0.0301 AC: 320 AN: 10622

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3592 AN: 68000

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.124 Hom.: 4146

Bravo AF: 0.279

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.39
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs2909679; hg19: chr7-131334612;