rs12782374

Variant names:

• chr10-94935594-G-A
• rs12782374

Your query was ambiguous. Multiple possible variants found:

• chr10-94935594-G-A
• chr10-94935594-G-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 0.143 in 152,140 control chromosomes in the GnomAD database, including 1,980 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 0.14 (1980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 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: 0.143 AC: 21783 AN: 152022 Hom.: 1977 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.143 AC: 21792 AN: 152140 Hom.: 1980 Cov.: 31 AF XY: 0.148 AC XY: 11033 AN XY: 74388

African (AFR) AF: 0.0522 AC: 2169 AN: 41536

American (AMR) AF: 0.128 AC: 1957 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5168

South Asian (SAS) AF: 0.319 AC: 1541 AN: 4830

European-Finnish (FIN) AF: 0.195 AC: 2059 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11493 AN: 67982

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.161 Hom.: 3043

Bravo AF: 0.130

Asia WGS AF: 0.294 AC: 1022 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.40
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12782374; hg19: chr10-96695351;