7-116511101-T-C

Position:

• chr7-116511101-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 0.491 in 151,836 control chromosomes in the GnomAD database, including 18,916 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 0.49 (18916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.491 AC: 74542 AN: 151718 Hom.: 18894 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.491 AC: 74606 AN: 151836 Hom.: 18916 Cov.: 31 AF XY: 0.499 AC XY: 37052 AN XY: 74206

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.502

Alfa AF: 0.495 Hom.: 28218

Bravo AF: 0.484

Asia WGS AF: 0.679 AC: 2356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6466579; hg19: chr7-116151155;