10-4282231-G-C

Variant names:

• chr10-4282231-G-C
• rs1022768

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 0.621 in 152,066 control chromosomes in the GnomAD database, including 30,204 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 0.62 (30204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94409 AN: 151948 Hom.: 30187 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.621 AC: 94467 AN: 152066 Hom.: 30204 Cov.: 32 AF XY: 0.619 AC XY: 46032 AN XY: 74328

African (AFR) AF: 0.608 AC: 25223 AN: 41458

American (AMR) AF: 0.607 AC: 9283 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3470

East Asian (EAS) AF: 0.123 AC: 636 AN: 5174

South Asian (SAS) AF: 0.467 AC: 2245 AN: 4812

European-Finnish (FIN) AF: 0.717 AC: 7578 AN: 10574

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45120 AN: 67974

Other (OTH) AF: 0.633 AC: 1338 AN: 2114

Alfa AF: 0.576 Hom.: 1885

Bravo AF: 0.607

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1022768; hg19: chr10-4324423;