7-15014253-G-C

Variant names:

• chr7-15014253-G-C
• rs2191346

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 0.394 in 151,802 control chromosomes in the GnomAD database, including 12,392 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 0.39 (12392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59814 AN: 151684 Hom.: 12398 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.394 AC: 59830 AN: 151802 Hom.: 12392 Cov.: 32 AF XY: 0.398 AC XY: 29555 AN XY: 74188

African (AFR) AF: 0.282 AC: 11673 AN: 41384

American (AMR) AF: 0.463 AC: 7049 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1380 AN: 5134

South Asian (SAS) AF: 0.372 AC: 1789 AN: 4806

European-Finnish (FIN) AF: 0.534 AC: 5625 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29335 AN: 67940

Other (OTH) AF: 0.408 AC: 861 AN: 2110

Alfa AF: 0.265 Hom.: 643

Bravo AF: 0.388

Asia WGS AF: 0.303 AC: 1055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2191346; hg19: chr7-15053878;