7-12673445-G-T

Variant names:

• chr7-12673445-G-T
• rs10488226

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 0.286 in 152,002 control chromosomes in the GnomAD database, including 7,251 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 0.29 (7251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 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: 0.286 AC: 43401 AN: 151886 Hom.: 7246 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.286 AC: 43399 AN: 152002 Hom.: 7251 Cov.: 32 AF XY: 0.283 AC XY: 21009 AN XY: 74296

African (AFR) AF: 0.121 AC: 5033 AN: 41472

American (AMR) AF: 0.261 AC: 3984 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3468

East Asian (EAS) AF: 0.148 AC: 767 AN: 5188

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4822

European-Finnish (FIN) AF: 0.354 AC: 3724 AN: 10520

Middle Eastern (MID) AF: 0.286 AC: 83 AN: 290

European-Non Finnish (NFE) AF: 0.382 AC: 25972 AN: 67948

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.351 Hom.: 43133

Bravo AF: 0.274

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10488226; hg19: chr7-12713070;