chr10-30753565-G-A

Variant names:

• chr10-30753565-G-A
• rs11008222

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 0.395 in 151,998 control chromosomes in the GnomAD database, including 13,027 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 0.39 (13027 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 7 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 = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59947 AN: 151880 Hom.: 13019 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.395 AC: 59985 AN: 151998 Hom.: 13027 Cov.: 31 AF XY: 0.390 AC XY: 28967 AN XY: 74284

African (AFR) AF: 0.240 AC: 9966 AN: 41464

American (AMR) AF: 0.382 AC: 5830 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1876 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5162

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4810

European-Finnish (FIN) AF: 0.335 AC: 3539 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33345 AN: 67948

Other (OTH) AF: 0.443 AC: 935 AN: 2112

Alfa AF: 0.465 Hom.: 43832

Bravo AF: 0.389

Asia WGS AF: 0.398 AC: 1380 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	0.37
DANN	Benign	0.64
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs11008222; hg19: chr10-31042494;