10-44501863-G-A

Variant names:

• chr10-44501863-G-A
• rs7919766

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 0.821 in 152,148 control chromosomes in the GnomAD database, including 51,375 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 0.82 (51375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.854 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: 0.821 AC: 124865 AN: 152030 Hom.: 51333 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.821 AC: 124963 AN: 152148 Hom.: 51375 Cov.: 32 AF XY: 0.824 AC XY: 61289 AN XY: 74398

African (AFR) AF: 0.777 AC: 32263 AN: 41498

American (AMR) AF: 0.866 AC: 13239 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3966 AN: 5156

South Asian (SAS) AF: 0.790 AC: 3814 AN: 4826

European-Finnish (FIN) AF: 0.855 AC: 9057 AN: 10592

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57124 AN: 68006

Other (OTH) AF: 0.841 AC: 1772 AN: 2106

Alfa AF: 0.829 Hom.: 7728

Bravo AF: 0.820

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.88
DANN	Benign	0.77
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs7919766; hg19: chr10-44997311;