17-71294528-C-T

Variant names:

• chr17-71294528-C-T
• rs4468671

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 0.661 in 152,030 control chromosomes in the GnomAD database, including 35,156 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 0.66 (35156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 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 = 0.785 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: 0.661 AC: 100386 AN: 151912 Hom.: 35143 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.661 AC: 100440 AN: 152030 Hom.: 35156 Cov.: 32 AF XY: 0.666 AC XY: 49491 AN XY: 74294

African (AFR) AF: 0.408 AC: 16896 AN: 41448

American (AMR) AF: 0.698 AC: 10652 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3770 AN: 5158

South Asian (SAS) AF: 0.806 AC: 3887 AN: 4820

European-Finnish (FIN) AF: 0.820 AC: 8673 AN: 10574

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51630 AN: 67996

Other (OTH) AF: 0.660 AC: 1393 AN: 2110

Alfa AF: 0.730 Hom.: 68546

Bravo AF: 0.638

Asia WGS AF: 0.779 AC: 2708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4468671; hg19: chr17-69290669;