rs2695234

Positions:

• chr4-24802616-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 0.786 in 152,178 control chromosomes in the GnomAD database, including 49,473 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 0.79 (49473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.912 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: 0.786 AC: 119527 AN: 152060 Hom.: 49469 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.786 AC: 119555 AN: 152178 Hom.: 49473 Cov.: 33 AF XY: 0.785 AC XY: 58432 AN XY: 74392

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.925

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.816

Alfa AF: 0.821 Hom.: 4945

Bravo AF: 0.766

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
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: rs2695234; hg19: chr4-24804238;