7-24502946-G-T

Variant names:

• chr7-24502946-G-T
• rs4719772

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 0.434 in 151,638 control chromosomes in the GnomAD database, including 14,675 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 0.43 (14675 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.434 AC: 65689 AN: 151520 Hom.: 14645 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.434 AC: 65759 AN: 151638 Hom.: 14675 Cov.: 31 AF XY: 0.446 AC XY: 33008 AN XY: 74080

African (AFR) AF: 0.405 AC: 16720 AN: 41312

American (AMR) AF: 0.448 AC: 6833 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1239 AN: 3460

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5166

South Asian (SAS) AF: 0.649 AC: 3123 AN: 4810

European-Finnish (FIN) AF: 0.528 AC: 5510 AN: 10432

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27409 AN: 67884

Other (OTH) AF: 0.423 AC: 890 AN: 2104

Alfa AF: 0.360 Hom.: 2189

Bravo AF: 0.427

Asia WGS AF: 0.654 AC: 2267 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.47
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs4719772; hg19: chr7-24542565;