17-54892240-C-T

Variant names:

• chr17-54892240-C-T
• rs2958919

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 0.889 in 152,136 control chromosomes in the GnomAD database, including 60,228 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 0.89 (60228 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 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: 0.889 AC: 135074 AN: 152016 Hom.: 60174 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.889 AC: 135188 AN: 152136 Hom.: 60228 Cov.: 31 AF XY: 0.889 AC XY: 66119 AN XY: 74364

African (AFR) AF: 0.946 AC: 39259 AN: 41498

American (AMR) AF: 0.866 AC: 13247 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3108 AN: 3468

East Asian (EAS) AF: 0.758 AC: 3911 AN: 5160

South Asian (SAS) AF: 0.846 AC: 4071 AN: 4812

European-Finnish (FIN) AF: 0.930 AC: 9845 AN: 10586

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58838 AN: 68006

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.871 Hom.: 46975

Bravo AF: 0.888

Asia WGS AF: 0.832 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2958919; hg19: chr17-52969601;