7-15013235-T-C

Variant names:

• chr7-15013235-T-C
• rs6960043

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 0.408 in 151,832 control chromosomes in the GnomAD database, including 14,050 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 0.41 (14050 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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: 0.409 AC: 61976 AN: 151712 Hom.: 14038 Cov.: 30

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.408 AC: 62006 AN: 151832 Hom.: 14050 Cov.: 30 AF XY: 0.404 AC XY: 29952 AN XY: 74158

African (AFR) AF: 0.221 AC: 9145 AN: 41406

American (AMR) AF: 0.378 AC: 5762 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1726 AN: 3464

East Asian (EAS) AF: 0.470 AC: 2400 AN: 5104

South Asian (SAS) AF: 0.530 AC: 2551 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4060 AN: 10550

Middle Eastern (MID) AF: 0.393 AC: 114 AN: 290

European-Non Finnish (NFE) AF: 0.514 AC: 34943 AN: 67952

Other (OTH) AF: 0.414 AC: 876 AN: 2116

Alfa AF: 0.299 Hom.: 1910

Bravo AF: 0.396

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.038
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6960043; hg19: chr7-15052860;