chr17-34285233-T-C

Variant names:

• chr17-34285233-T-C
• rs4795896

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 0.141 in 152,000 control chromosomes in the GnomAD database, including 2,534 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 0.14 (2534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.140 AC: 21339 AN: 151880 Hom.: 2518 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.141 AC: 21378 AN: 152000 Hom.: 2534 Cov.: 31 AF XY: 0.146 AC XY: 10879 AN XY: 74296

African (AFR) AF: 0.0553 AC: 2293 AN: 41494

American (AMR) AF: 0.323 AC: 4924 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2849 AN: 5144

South Asian (SAS) AF: 0.180 AC: 866 AN: 4804

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8245 AN: 67958

Other (OTH) AF: 0.134 AC: 281 AN: 2104

Alfa AF: 0.118 Hom.: 216

Bravo AF: 0.155

Asia WGS AF: 0.355 AC: 1230 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	2.6
DANN	Benign	0.76
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs4795896; hg19: chr17-32612252;