10-12303441-C-T

Variant names:

• chr10-12303441-C-T
• rs11257695

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 0.322 in 151,928 control chromosomes in the GnomAD database, including 9,465 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 0.32 (9465 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.467 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: 0.322 AC: 48845 AN: 151808 Hom.: 9461 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.322 AC: 48852 AN: 151928 Hom.: 9465 Cov.: 31 AF XY: 0.326 AC XY: 24189 AN XY: 74230

African (AFR) AF: 0.108 AC: 4472 AN: 41460

American (AMR) AF: 0.288 AC: 4391 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1637 AN: 5154

South Asian (SAS) AF: 0.484 AC: 2329 AN: 4814

European-Finnish (FIN) AF: 0.511 AC: 5388 AN: 10546

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28067 AN: 67942

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.384 Hom.: 11700

Bravo AF: 0.295

Asia WGS AF: 0.399 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.77
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11257695; hg19: chr10-12345440;