4-24802616-A-G

Variant names:

• chr4-24802616-A-G
• rs2695234

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 0.786 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.499 AC: 20706 AN: 41466

American (AMR) AF: 0.811 AC: 12396 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3033 AN: 3466

East Asian (EAS) AF: 0.801 AC: 4145 AN: 5178

South Asian (SAS) AF: 0.855 AC: 4121 AN: 4818

European-Finnish (FIN) AF: 0.925 AC: 9821 AN: 10618

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62480 AN: 68022

Other (OTH) AF: 0.816 AC: 1726 AN: 2114

Alfa AF: 0.888 Hom.: 35403

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2695234; hg19: chr4-24804238;