chr17-69381921-T-G

Variant names:

• chr17-69381921-T-G
• rs817097

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 0.357 in 151,370 control chromosomes in the GnomAD database, including 10,100 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 0.36 (10100 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.357 AC: 53936 AN: 151268 Hom.: 10093 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.357 AC: 53976 AN: 151370 Hom.: 10100 Cov.: 31 AF XY: 0.351 AC XY: 25945 AN XY: 73938

African (AFR) AF: 0.459 AC: 18951 AN: 41282

American (AMR) AF: 0.271 AC: 4120 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3468

East Asian (EAS) AF: 0.142 AC: 733 AN: 5152

South Asian (SAS) AF: 0.271 AC: 1303 AN: 4812

European-Finnish (FIN) AF: 0.285 AC: 2953 AN: 10356

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23566 AN: 67810

Other (OTH) AF: 0.367 AC: 770 AN: 2098

Alfa AF: 0.347 Hom.: 26503

Bravo AF: 0.359

Asia WGS AF: 0.263 AC: 916 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	1.4
DANN	Benign	0.31
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs817097; hg19: chr17-67378062;