17-70262067-G-T

Variant names:

• chr17-70262067-G-T
• rs992072

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 0.663 in 152,006 control chromosomes in the GnomAD database, including 33,867 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 (33867 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 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: 0.663 AC: 100691 AN: 151888 Hom.: 33847 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.663 AC: 100754 AN: 152006 Hom.: 33867 Cov.: 32 AF XY: 0.667 AC XY: 49548 AN XY: 74288

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.672

Alfa AF: 0.639 Hom.: 3444

Bravo AF: 0.642

Asia WGS AF: 0.671 AC: 2335 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	4.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs992072; hg19: chr17-68258208;