10-44020973-G-A

Variant names:

• chr10-44020973-G-A
• rs9332446

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 0.39 in 152,044 control chromosomes in the GnomAD database, including 13,363 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 (13363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 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: 0.390 AC: 59226 AN: 151926 Hom.: 13358 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.390 AC: 59238 AN: 152044 Hom.: 13363 Cov.: 32 AF XY: 0.388 AC XY: 28866 AN XY: 74306

African (AFR) AF: 0.156 AC: 6476 AN: 41478

American (AMR) AF: 0.360 AC: 5504 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2589 AN: 5152

South Asian (SAS) AF: 0.382 AC: 1832 AN: 4802

European-Finnish (FIN) AF: 0.457 AC: 4845 AN: 10592

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34835 AN: 67966

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.431 Hom.: 2037

Bravo AF: 0.372

Asia WGS AF: 0.422 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.43
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9332446; hg19: chr10-44516421;