7-12153118-T-C

Variant names:

• chr7-12153118-T-C
• rs7795554

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 0.332 in 151,896 control chromosomes in the GnomAD database, including 8,729 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 0.33 (8729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.332 AC: 50337 AN: 151778 Hom.: 8720 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.332 AC: 50373 AN: 151896 Hom.: 8729 Cov.: 32 AF XY: 0.327 AC XY: 24247 AN XY: 74234

African (AFR) AF: 0.332 AC: 13763 AN: 41472

American (AMR) AF: 0.266 AC: 4057 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.0589 AC: 304 AN: 5162

South Asian (SAS) AF: 0.194 AC: 934 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3616 AN: 10562

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25177 AN: 67860

Other (OTH) AF: 0.327 AC: 687 AN: 2104

Alfa AF: 0.357 Hom.: 30959

Bravo AF: 0.330

Asia WGS AF: 0.160 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.53
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs7795554; hg19: chr7-12192744;