7-54121112-T-C

Variant names:

• chr7-54121112-T-C
• rs10247013

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 0.287 in 151,932 control chromosomes in the GnomAD database, including 6,613 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 0.29 (6613 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.287 AC: 43556 AN: 151814 Hom.: 6597 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.287 AC: 43611 AN: 151932 Hom.: 6613 Cov.: 33 AF XY: 0.292 AC XY: 21655 AN XY: 74250

African (AFR) AF: 0.364 AC: 15022 AN: 41310

American (AMR) AF: 0.307 AC: 4688 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1254 AN: 5176

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4824

European-Finnish (FIN) AF: 0.325 AC: 3436 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16604 AN: 67980

Other (OTH) AF: 0.240 AC: 506 AN: 2106

Alfa AF: 0.253 Hom.: 2809

Bravo AF: 0.290

Asia WGS AF: 0.278 AC: 966 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.056
DANN	Benign	0.32
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10247013; hg19: chr7-54188805;