17-55680426-T-C

Variant names:

• chr17-55680426-T-C
• rs1549519
• ENST00000847279.1:n.245-10457T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000847279.1(ENSG00000289016):​n.245-10457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000289016 ENST00000847279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 13 publications found

Genes affected

ENSG00000289016 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847279.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289016	ENST00000847279.1		n.245-10457T>C		intron	N/A
	ENSG00000289016	ENST00000847280.1		n.251-3609T>C		intron	N/A

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

African (AFR) AF: 0.813 AC: 33725 AN: 41458

American (AMR) AF: 0.466 AC: 7113 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2299 AN: 5152

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4814

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10580

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11632 AN: 67954

Other (OTH) AF: 0.372 AC: 785 AN: 2108

Alfa AF: 0.240 Hom.: 28728

Bravo AF: 0.437

Asia WGS AF: 0.367 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.33
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1549519;

hg19: chr17-53757787;