rs724749

Positions:

• chr4-124804199-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 0.635 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;