10-106003475-A-G

Variant names:

• chr10-106003475-A-G
• rs1361356

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 0.654 in 152,002 control chromosomes in the GnomAD database, including 33,934 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 0.65 (33934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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: 0.654 AC: 99282 AN: 151884 Hom.: 33879 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.654 AC: 99394 AN: 152002 Hom.: 33934 Cov.: 31 AF XY: 0.649 AC XY: 48227 AN XY: 74292

African (AFR) AF: 0.866 AC: 35889 AN: 41466

American (AMR) AF: 0.653 AC: 9973 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1868 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3681 AN: 5160

South Asian (SAS) AF: 0.438 AC: 2111 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5917 AN: 10552

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37963 AN: 67956

Other (OTH) AF: 0.632 AC: 1334 AN: 2110

Alfa AF: 0.548 Hom.: 10007

Bravo AF: 0.674

Asia WGS AF: 0.601 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.64
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1361356; hg19: chr10-107763233;