17-43763434-C-T

Variant names:

• chr17-43763434-C-T
• rs1234612

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 0.705 in 151,890 control chromosomes in the GnomAD database, including 37,928 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 0.70 (37928 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.13
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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: 0.705 AC: 106991 AN: 151772 Hom.: 37905 Cov.: 30

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.705 AC: 107064 AN: 151890 Hom.: 37928 Cov.: 30 AF XY: 0.709 AC XY: 52656 AN XY: 74244

African (AFR) AF: 0.638 AC: 26382 AN: 41374

American (AMR) AF: 0.771 AC: 11788 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2044 AN: 3462

East Asian (EAS) AF: 0.847 AC: 4382 AN: 5172

South Asian (SAS) AF: 0.714 AC: 3441 AN: 4820

European-Finnish (FIN) AF: 0.762 AC: 8014 AN: 10522

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48662 AN: 67946

Other (OTH) AF: 0.694 AC: 1465 AN: 2112

Alfa AF: 0.706 Hom.: 70148

Bravo AF: 0.700

Asia WGS AF: 0.789 AC: 2746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.86
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs1234612; hg19: chr17-41840802;