chr17-71290540-T-G

Position:

• chr17-71290540-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.638 in 151,956 control chromosomes in the GnomAD database, including 33,942 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 0.64 (33942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96955 AN: 151838 Hom.: 33935 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.638 AC: 96974 AN: 151956 Hom.: 33942 Cov.: 31 AF XY: 0.644 AC XY: 47842 AN XY: 74250

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.652

Alfa AF: 0.746 Hom.: 82351

Bravo AF: 0.612

Asia WGS AF: 0.778 AC: 2701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11077554; hg19: chr17-69286681;