4-38743861-T-C

Variant names:

• chr4-38743861-T-C
• rs10008032

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 0.67 in 152,066 control chromosomes in the GnomAD database, including 37,414 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 0.67 (37414 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101769 AN: 151950 Hom.: 37344 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.670 AC: 101900 AN: 152066 Hom.: 37414 Cov.: 31 AF XY: 0.676 AC XY: 50226 AN XY: 74322

African (AFR) AF: 0.915 AC: 38001 AN: 41512

American (AMR) AF: 0.760 AC: 11602 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5175 AN: 5190

South Asian (SAS) AF: 0.908 AC: 4374 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10548

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33683 AN: 67946

Other (OTH) AF: 0.721 AC: 1522 AN: 2110

Alfa AF: 0.584 Hom.: 16040

Bravo AF: 0.700

Asia WGS AF: 0.946 AC: 3290 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	0.018
DANN	Benign	0.72
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10008032; hg19: chr4-38745482;