17-34254988-G-C

Variant names:

• chr17-34254988-G-C
• rs2857656

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.343 in 151,906 control chromosomes in the GnomAD database, including 9,529 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 0.34 (9529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 62 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52103 AN: 151788 Hom.: 9508 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.343 AC: 52170 AN: 151906 Hom.: 9529 Cov.: 32 AF XY: 0.350 AC XY: 25960 AN XY: 74218

African (AFR) AF: 0.398 AC: 16503 AN: 41422

American (AMR) AF: 0.453 AC: 6915 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2848 AN: 5138

South Asian (SAS) AF: 0.344 AC: 1654 AN: 4812

European-Finnish (FIN) AF: 0.343 AC: 3608 AN: 10518

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

European-Non Finnish (NFE) AF: 0.276 AC: 18754 AN: 67976

Other (OTH) AF: 0.327 AC: 691 AN: 2110

Alfa AF: 0.175 Hom.: 365

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		1.2
PromoterAI		-0.029	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2857656; hg19: chr17-32582007;