rs2037046

Variant names:

• chr4-56808215-G-A
• rs2037046

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 0.642 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

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 (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

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.632

Alfa AF: 0.599 Hom.: 15280

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037046; hg19: chr4-57674381;