7-8933241-T-C

Variant names:

• chr7-8933241-T-C
• rs7776800

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 0.354 in 146,676 control chromosomes in the GnomAD database, including 9,333 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 0.35 (9333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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: 0.354 AC: 51860 AN: 146552 Hom.: 9325 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.354 AC: 51928 AN: 146676 Hom.: 9333 Cov.: 32 AF XY: 0.348 AC XY: 24874 AN XY: 71386

African (AFR) AF: 0.423 AC: 17446 AN: 41258

American (AMR) AF: 0.360 AC: 5244 AN: 14562

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1186 AN: 3390

East Asian (EAS) AF: 0.0992 AC: 448 AN: 4518

South Asian (SAS) AF: 0.218 AC: 996 AN: 4570

European-Finnish (FIN) AF: 0.309 AC: 2962 AN: 9576

Middle Eastern (MID) AF: 0.372 AC: 105 AN: 282

European-Non Finnish (NFE) AF: 0.343 AC: 22502 AN: 65596

Other (OTH) AF: 0.356 AC: 724 AN: 2032

Alfa AF: 0.373 Hom.: 2401

Bravo AF: 0.351

Asia WGS AF: 0.220 AC: 705 AN: 3210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	0.0090
DANN	Benign	0.57
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7776800; hg19: chr7-8972871;