17-73181649-C-T

Position:

• chr17-73181649-C-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000264860	ENST00000580671.1	n.313-6190C>T		intron_variant		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;