chr17-43760292-T-C

Variant names:

• chr17-43760292-T-C
• rs2023794

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 0.0609 in 152,274 control chromosomes in the GnomAD database, including 410 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 0.061 (410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 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: 0.0610 AC: 9280 AN: 152154 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0609 AC: 9281 AN: 152274 Hom.: 410 Cov.: 32 AF XY: 0.0625 AC XY: 4651 AN XY: 74458

African (AFR) AF: 0.0161 AC: 668 AN: 41564

American (AMR) AF: 0.139 AC: 2127 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3466

East Asian (EAS) AF: 0.0804 AC: 417 AN: 5184

South Asian (SAS) AF: 0.129 AC: 624 AN: 4822

European-Finnish (FIN) AF: 0.0497 AC: 527 AN: 10612

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

European-Non Finnish (NFE) AF: 0.0678 AC: 4610 AN: 68018

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0686 Hom.: 750

Bravo AF: 0.0663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs2023794; hg19: chr17-41837660;