4-38181053-A-G

Variant names:

• chr4-38181053-A-G
• rs663677

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 0.676 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.674 AC: 27964 AN: 41476

American (AMR) AF: 0.608 AC: 9276 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1954 AN: 3464

East Asian (EAS) AF: 0.557 AC: 2884 AN: 5174

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4822

European-Finnish (FIN) AF: 0.760 AC: 8045 AN: 10586

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47339 AN: 67988

Other (OTH) AF: 0.626 AC: 1320 AN: 2108

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs663677; hg19: chr4-38182674;