17-55680426-T-C

Variant names:

• chr17-55680426-T-C
• rs1549519

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 0.388 in 152,004 control chromosomes in the GnomAD database, including 17,593 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 0.39 (17593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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: 0.388 AC: 58949 AN: 151886 Hom.: 17540 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.388 AC: 59052 AN: 152004 Hom.: 17593 Cov.: 32 AF XY: 0.385 AC XY: 28570 AN XY: 74304

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.372

Alfa AF: 0.208 Hom.: 9168

Bravo AF: 0.437

Asia WGS AF: 0.367 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549519; hg19: chr17-53757787;