4-38764099-C-T

Variant names:

• chr4-38764099-C-T
• rs10008492

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 0.598 in 152,124 control chromosomes in the GnomAD database, including 32,125 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 0.60 (32125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90875 AN: 152006 Hom.: 32050 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.598 AC: 91011 AN: 152124 Hom.: 32125 Cov.: 32 AF XY: 0.608 AC XY: 45219 AN XY: 74378

African (AFR) AF: 0.894 AC: 37080 AN: 41492

American (AMR) AF: 0.711 AC: 10875 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5171 AN: 5186

South Asian (SAS) AF: 0.918 AC: 4427 AN: 4820

European-Finnish (FIN) AF: 0.346 AC: 3664 AN: 10576

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25624 AN: 67964

Other (OTH) AF: 0.661 AC: 1398 AN: 2114

Alfa AF: 0.474 Hom.: 32259

Bravo AF: 0.632

Asia WGS AF: 0.938 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.052
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10008492; hg19: chr4-38765720;