chr7-116510815-C-T

Variant names:

• chr7-116510815-C-T
• rs6466578

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 0.845 in 152,196 control chromosomes in the GnomAD database, including 54,397 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 0.84 (54397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.845 AC: 128451 AN: 152078 Hom.: 54355 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.845 AC: 128552 AN: 152196 Hom.: 54397 Cov.: 32 AF XY: 0.848 AC XY: 63093 AN XY: 74404

African (AFR) AF: 0.816 AC: 33857 AN: 41500

American (AMR) AF: 0.868 AC: 13262 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3021 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4909 AN: 5184

South Asian (SAS) AF: 0.866 AC: 4179 AN: 4826

European-Finnish (FIN) AF: 0.879 AC: 9313 AN: 10594

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57227 AN: 68018

Other (OTH) AF: 0.846 AC: 1786 AN: 2112

Alfa AF: 0.843 Hom.: 7754

Bravo AF: 0.843

Asia WGS AF: 0.891 AC: 3080 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.37
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6466578; hg19: chr7-116150869;