7-100914499-C-T

Variant names:

• chr7-100914499-C-T
• rs6976053

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 0.414 in 151,882 control chromosomes in the GnomAD database, including 15,142 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 0.41 (15142 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.414 AC: 62868 AN: 151764 Hom.: 15133 Cov.: 30

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.414 AC: 62890 AN: 151882 Hom.: 15142 Cov.: 30 AF XY: 0.422 AC XY: 31334 AN XY: 74192

African (AFR) AF: 0.178 AC: 7393 AN: 41440

American (AMR) AF: 0.579 AC: 8826 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4253 AN: 5146

South Asian (SAS) AF: 0.526 AC: 2533 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5126 AN: 10536

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31521 AN: 67924

Other (OTH) AF: 0.449 AC: 947 AN: 2110

Alfa AF: 0.451 Hom.: 34789

Bravo AF: 0.415

Asia WGS AF: 0.642 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.56
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6976053; hg19: chr7-100512119;