7-112522672-C-T

Variant names:

• chr7-112522672-C-T
• rs3095039

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.461 in 151,958 control chromosomes in the GnomAD database, including 17,751 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 0.46 (17751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.461 AC: 70000 AN: 151840 Hom.: 17729 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.461 AC: 70075 AN: 151958 Hom.: 17751 Cov.: 32 AF XY: 0.463 AC XY: 34416 AN XY: 74256

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.414

Alfa AF: 0.419 Hom.: 2429

Bravo AF: 0.477

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095039; hg19: chr7-112162727;