chr7-81802463-C-T

Variant names:

• chr7-81802463-C-T
• rs9332389

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 0.345 in 151,964 control chromosomes in the GnomAD database, including 9,703 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 (9703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.345 AC: 52405 AN: 151846 Hom.: 9689 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.345 AC: 52446 AN: 151964 Hom.: 9703 Cov.: 32 AF XY: 0.346 AC XY: 25717 AN XY: 74254

African (AFR) AF: 0.225 AC: 9344 AN: 41460

American (AMR) AF: 0.461 AC: 7026 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2331 AN: 5154

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4047 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26264 AN: 67962

Other (OTH) AF: 0.359 AC: 756 AN: 2106

Alfa AF: 0.362 Hom.: 3498

Bravo AF: 0.348

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9332389; hg19: chr7-81431779;