chr7-12153806-G-A

Variant names:

• chr7-12153806-G-A
• rs114945094

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 0.331 in 151,514 control chromosomes in the GnomAD database, including 8,606 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 (8606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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: 0.331 AC: 50072 AN: 151396 Hom.: 8597 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.331 AC: 50108 AN: 151514 Hom.: 8606 Cov.: 32 AF XY: 0.326 AC XY: 24112 AN XY: 74054

African (AFR) AF: 0.331 AC: 13673 AN: 41332

American (AMR) AF: 0.266 AC: 4051 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1267 AN: 3460

East Asian (EAS) AF: 0.0593 AC: 307 AN: 5180

South Asian (SAS) AF: 0.194 AC: 931 AN: 4802

European-Finnish (FIN) AF: 0.343 AC: 3604 AN: 10514

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

European-Non Finnish (NFE) AF: 0.370 AC: 25040 AN: 67690

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

Alfa AF: 0.345 Hom.: 1089

Bravo AF: 0.330

Asia WGS AF: 0.158 AC: 551 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.17
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs114945094; hg19: chr7-12193432;