4-40728486-A-G

Position:

• chr4-40728486-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 0.561 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.595

Alfa AF: 0.607 Hom.: 42796

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790142; hg19: chr4-40730503;