4-40728486-A-G

Variant names:

• chr4-40728486-A-G
• rs790142

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 0.561 in 151,948 control chromosomes in the GnomAD database, including 24,582 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 0.56 (24582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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: 0.562 AC: 85275 AN: 151830 Hom.: 24581 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.561 AC: 85312 AN: 151948 Hom.: 24582 Cov.: 32 AF XY: 0.562 AC XY: 41713 AN XY: 74244

African (AFR) AF: 0.453 AC: 18770 AN: 41416

American (AMR) AF: 0.506 AC: 7720 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.789 AC: 4079 AN: 5170

South Asian (SAS) AF: 0.552 AC: 2663 AN: 4824

European-Finnish (FIN) AF: 0.610 AC: 6428 AN: 10536

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41581 AN: 67968

Other (OTH) AF: 0.595 AC: 1256 AN: 2110

Alfa AF: 0.596 Hom.: 94617

Bravo AF: 0.551

Asia WGS AF: 0.648 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.1
DANN	Benign	0.68
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs790142; hg19: chr4-40730503;