7-12556990-T-C

Position:

• chr7-12556990-T-C

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 0.611 in 151,932 control chromosomes in the GnomAD database, including 28,443 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 0.61 (28443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92739 AN: 151814 Hom.: 28412 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.611 AC: 92814 AN: 151932 Hom.: 28443 Cov.: 31 AF XY: 0.606 AC XY: 44989 AN XY: 74242

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.596

Alfa AF: 0.613 Hom.: 35707

Bravo AF: 0.622

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11764174; hg19: chr7-12596616;