4-38181053-A-G

Position:

• chr4-38181053-A-G

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 0.676 in 152,090 control chromosomes in the GnomAD database, including 35,045 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 0.68 (35045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102805 AN: 151972 Hom.: 35042 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.676 AC: 102834 AN: 152090 Hom.: 35045 Cov.: 32 AF XY: 0.679 AC XY: 50519 AN XY: 74350

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.626

Alfa AF: 0.682 Hom.: 5611

Bravo AF: 0.657

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs663677; hg19: chr4-38182674;