chr4-24696680-G-C

Variant names:

• chr4-24696680-G-C
• rs4697472

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 0.481 in 152,010 control chromosomes in the GnomAD database, including 17,844 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 0.48 (17844 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 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: 0.481 AC: 73013 AN: 151892 Hom.: 17831 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.481 AC: 73071 AN: 152010 Hom.: 17844 Cov.: 32 AF XY: 0.489 AC XY: 36329 AN XY: 74292

African (AFR) AF: 0.494 AC: 20462 AN: 41448

American (AMR) AF: 0.562 AC: 8589 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3315 AN: 5178

South Asian (SAS) AF: 0.613 AC: 2954 AN: 4818

European-Finnish (FIN) AF: 0.497 AC: 5245 AN: 10548

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29386 AN: 67962

Other (OTH) AF: 0.448 AC: 946 AN: 2112

Alfa AF: 0.306 Hom.: 747

Bravo AF: 0.487

Asia WGS AF: 0.577 AC: 2004 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.37
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs4697472; hg19: chr4-24698303;