chr10-44627931-T-C

Variant names:

• chr10-44627931-T-C
• rs11239177

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 0.469 in 152,014 control chromosomes in the GnomAD database, including 16,930 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 0.47 (16930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 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: 0.469 AC: 71193 AN: 151894 Hom.: 16900 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.469 AC: 71284 AN: 152014 Hom.: 16930 Cov.: 32 AF XY: 0.468 AC XY: 34765 AN XY: 74286

African (AFR) AF: 0.473 AC: 19618 AN: 41466

American (AMR) AF: 0.505 AC: 7710 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1718 AN: 5178

South Asian (SAS) AF: 0.474 AC: 2283 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5110 AN: 10538

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31778 AN: 67956

Other (OTH) AF: 0.463 AC: 977 AN: 2110

Alfa AF: 0.461 Hom.: 69917

Bravo AF: 0.475

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.89
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs11239177; hg19: chr10-45123379;