7-15024684-G-T

Variant names:

• chr7-15024684-G-T
• rs2191349

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 0.545 in 151,844 control chromosomes in the GnomAD database, including 22,800 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 0.54 (22800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.545 AC: 82623 AN: 151724 Hom.: 22786 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.545 AC: 82687 AN: 151844 Hom.: 22800 Cov.: 32 AF XY: 0.541 AC XY: 40116 AN XY: 74204

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.540

Alfa AF: 0.545 Hom.: 34360

Bravo AF: 0.546

Asia WGS AF: 0.641 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2191349; hg19: chr7-15064309;