17-73181649-C-T

Variant names:

• chr17-73181649-C-T
• rs4969017
• ENST00000580671.1:n.313-6190C>T

Variant summary

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

The ENST00000580671.1(ENSG00000264860):​n.313-6190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 151,934 control chromosomes in the GnomAD database, including 63,370 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 0.91 (63370 hom., cov: 29)
• Consequence: ENSG00000264860 ENST00000580671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

Genes affected

ENSG00000264860 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.984 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
ENSG00000264860	ENST00000580671.1	n.313-6190C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137698 AN: 151816 Hom.: 63327 Cov.: 29

Gnomad AFR AF: 0.734

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.907 AC: 137792 AN: 151934 Hom.: 63370 Cov.: 29 AF XY: 0.907 AC XY: 67338 AN XY: 74280

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.912

Alfa AF: 0.918 Hom.: 8889

Bravo AF: 0.895

Asia WGS AF: 0.881 AC: 3063 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	0.26
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4969017; hg19: chr17-71177788;