chr4-56808215-G-A

Variant names:

• chr4-56808215-G-A
• rs2037046

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 0.642 in 151,768 control chromosomes in the GnomAD database, including 31,830 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 0.64 (31830 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.642 AC: 97338 AN: 151648 Hom.: 31812 Cov.: 30

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.642 AC: 97403 AN: 151768 Hom.: 31830 Cov.: 30 AF XY: 0.643 AC XY: 47716 AN XY: 74158

African (AFR) AF: 0.743 AC: 30775 AN: 41400

American (AMR) AF: 0.681 AC: 10359 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3654 AN: 5138

South Asian (SAS) AF: 0.547 AC: 2621 AN: 4792

European-Finnish (FIN) AF: 0.617 AC: 6496 AN: 10524

Middle Eastern (MID) AF: 0.545 AC: 158 AN: 290

European-Non Finnish (NFE) AF: 0.584 AC: 39684 AN: 67934

Other (OTH) AF: 0.632 AC: 1330 AN: 2104

Alfa AF: 0.604 Hom.: 25558

Bravo AF: 0.656

Asia WGS AF: 0.585 AC: 2031 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	0.75
DANN	Benign	0.72
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2037046; hg19: chr4-57674381;