7-12095708-C-T

Position:

• chr7-12095708-C-T

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 0.802 in 152,044 control chromosomes in the GnomAD database, including 49,103 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 0.80 (49103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121849 AN: 151926 Hom.: 49057 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.802 AC: 121955 AN: 152044 Hom.: 49103 Cov.: 31 AF XY: 0.800 AC XY: 59493 AN XY: 74334

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.786

Alfa AF: 0.808 Hom.: 33124

Bravo AF: 0.799

Asia WGS AF: 0.683 AC: 2368 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10226395; hg19: chr7-12135334;