chr17-71374289-G-T

Variant names:

• chr17-71374289-G-T
• rs17225585

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 0.108 in 152,098 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 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: 0.108 AC: 16486 AN: 151980 Hom.: 1039 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.108 AC: 16491 AN: 152098 Hom.: 1040 Cov.: 32 AF XY: 0.114 AC XY: 8485 AN XY: 74344

African (AFR) AF: 0.0478 AC: 1984 AN: 41522

American (AMR) AF: 0.119 AC: 1825 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1284 AN: 5170

South Asian (SAS) AF: 0.191 AC: 917 AN: 4812

European-Finnish (FIN) AF: 0.184 AC: 1938 AN: 10530

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7805 AN: 68004

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.110 Hom.: 2804

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17225585; hg19: chr17-69370430;