17-81184262-G-T

Variant names:

• chr17-81184262-G-T
• rs7225354

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 0.0946 in 152,124 control chromosomes in the GnomAD database, including 1,007 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 0.095 (1007 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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: 0.0944 AC: 14354 AN: 152006 Hom.: 998 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0946 AC: 14394 AN: 152124 Hom.: 1007 Cov.: 33 AF XY: 0.0938 AC XY: 6971 AN XY: 74350

African (AFR) AF: 0.186 AC: 7727 AN: 41490

American (AMR) AF: 0.0483 AC: 739 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.162 AC: 828 AN: 5120

South Asian (SAS) AF: 0.126 AC: 610 AN: 4824

European-Finnish (FIN) AF: 0.0446 AC: 473 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0502 AC: 3413 AN: 67992

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.0554 Hom.: 167

Bravo AF: 0.0986

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.27
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs7225354; hg19: chr17-79158062;