4-40366831-G-A

Variant names:

• chr4-40366831-G-A
• rs10021851

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 0.405 in 152,040 control chromosomes in the GnomAD database, including 13,865 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 0.41 (13865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 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: 0.405 AC: 61561 AN: 151924 Hom.: 13855 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.405 AC: 61588 AN: 152040 Hom.: 13865 Cov.: 33 AF XY: 0.410 AC XY: 30457 AN XY: 74310

African (AFR) AF: 0.207 AC: 8590 AN: 41486

American (AMR) AF: 0.437 AC: 6668 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3466

East Asian (EAS) AF: 0.770 AC: 3985 AN: 5178

South Asian (SAS) AF: 0.551 AC: 2662 AN: 4828

European-Finnish (FIN) AF: 0.443 AC: 4671 AN: 10534

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.468 AC: 31808 AN: 67978

Other (OTH) AF: 0.422 AC: 891 AN: 2110

Alfa AF: 0.460 Hom.: 25854

Bravo AF: 0.396

Asia WGS AF: 0.619 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.70
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10021851; hg19: chr4-40368848;