17-34260706-C-T

Variant names:

• chr17-34260706-C-T
• rs991804

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 0.334 in 152,018 control chromosomes in the GnomAD database, including 8,991 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 0.33 (8991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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: 0.334 AC: 50750 AN: 151898 Hom.: 8970 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.334 AC: 50811 AN: 152018 Hom.: 8991 Cov.: 32 AF XY: 0.340 AC XY: 25297 AN XY: 74294

African (AFR) AF: 0.366 AC: 15182 AN: 41444

American (AMR) AF: 0.450 AC: 6884 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2852 AN: 5154

South Asian (SAS) AF: 0.342 AC: 1647 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3615 AN: 10536

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18759 AN: 67996

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.297 Hom.: 21831

Bravo AF: 0.345

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs991804; hg19: chr17-32587725;