4-38743861-T-C

Variant names:

• chr4-38743861-T-C
• rs10008032

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.670 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

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.721

Alfa AF: 0.590 Hom.: 14906

Bravo AF: 0.700

Asia WGS AF: 0.946 AC: 3290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.018
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10008032; hg19: chr4-38745482;