rs724749

Variant names:

• chr4-124804199-A-G
• rs724749

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 0.635 in 152,002 control chromosomes in the GnomAD database, including 31,344 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 0.63 (31344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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 = 0.779 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: 0.634 AC: 96352 AN: 151884 Hom.: 31305 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.635 AC: 96454 AN: 152002 Hom.: 31344 Cov.: 32 AF XY: 0.628 AC XY: 46615 AN XY: 74276

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.620

Alfa AF: 0.607 Hom.: 6719

Bravo AF: 0.644

Asia WGS AF: 0.494 AC: 1718 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	3.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724749; hg19: chr4-125725354;