17-43759255-C-T

Variant names:

• chr17-43759255-C-T
• rs851054

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 0.614 in 151,968 control chromosomes in the GnomAD database, including 28,912 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 0.61 (28912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 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: 0.614 AC: 93193 AN: 151850 Hom.: 28877 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.614 AC: 93275 AN: 151968 Hom.: 28912 Cov.: 32 AF XY: 0.617 AC XY: 45820 AN XY: 74262

African (AFR) AF: 0.582 AC: 24097 AN: 41414

American (AMR) AF: 0.561 AC: 8568 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2156 AN: 3464

East Asian (EAS) AF: 0.384 AC: 1981 AN: 5158

South Asian (SAS) AF: 0.656 AC: 3164 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7908 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43456 AN: 67954

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.551 Hom.: 2651

Bravo AF: 0.593

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.9
DANN	Benign	0.90
PhyloP100		-0.40
PromoterAI		-0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs851054; hg19: chr17-41836623;