17-43759814-G-C

Variant names:

• chr17-43759814-G-C
• rs851056

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.641 in 151,134 control chromosomes in the GnomAD database, including 31,261 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 0.64 (31261 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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: 0.640 AC: 96709 AN: 151014 Hom.: 31215 Cov.: 27

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.641 AC: 96809 AN: 151134 Hom.: 31261 Cov.: 27 AF XY: 0.644 AC XY: 47532 AN XY: 73798

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.606

Alfa AF: 0.645 Hom.: 3734

Bravo AF: 0.623

Asia WGS AF: 0.528 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs851056; hg19: chr17-41837182;