rs13228784

Variant names:

• chr7-95331513-A-G
• rs13228784

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 0.256 in 151,996 control chromosomes in the GnomAD database, including 5,407 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 0.26 (5407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 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: 0.256 AC: 38865 AN: 151878 Hom.: 5399 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.256 AC: 38889 AN: 151996 Hom.: 5407 Cov.: 32 AF XY: 0.264 AC XY: 19627 AN XY: 74298

African (AFR) AF: 0.228 AC: 9435 AN: 41472

American (AMR) AF: 0.212 AC: 3232 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3470

East Asian (EAS) AF: 0.139 AC: 719 AN: 5184

South Asian (SAS) AF: 0.364 AC: 1760 AN: 4830

European-Finnish (FIN) AF: 0.435 AC: 4574 AN: 10526

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17522 AN: 67922

Other (OTH) AF: 0.235 AC: 497 AN: 2114

Alfa AF: 0.244 Hom.: 7350

Bravo AF: 0.233

Asia WGS AF: 0.261 AC: 904 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.48
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13228784; hg19: chr7-94960825;