17-34645710-T-C

Variant names:

• chr17-34645710-T-C
• rs4990638

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 0.0957 in 152,006 control chromosomes in the GnomAD database, including 760 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 0.096 (760 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 3 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 = 0.161 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14537 AN: 151888 Hom.: 760 Cov.: 33

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0957 AC: 14544 AN: 152006 Hom.: 760 Cov.: 33 AF XY: 0.0954 AC XY: 7087 AN XY: 74274

African (AFR) AF: 0.0940 AC: 3899 AN: 41472

American (AMR) AF: 0.0898 AC: 1373 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3468

East Asian (EAS) AF: 0.170 AC: 871 AN: 5114

South Asian (SAS) AF: 0.0644 AC: 310 AN: 4810

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10590

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6584 AN: 67942

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.0912 Hom.: 1226

Bravo AF: 0.0952

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4990638; hg19: chr17-32972729;