17-73181649-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000264860 (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 (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580671.1. 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
	ENSG00000264860	ENST00000580671.1	TSL:4	n.313-6190C>T		intron	N/A

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

African (AFR) AF: 0.734 AC: 30333 AN: 41336

American (AMR) AF: 0.951 AC: 14505 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3293 AN: 3472

East Asian (EAS) AF: 0.849 AC: 4371 AN: 5148

South Asian (SAS) AF: 0.930 AC: 4460 AN: 4798

European-Finnish (FIN) AF: 0.980 AC: 10373 AN: 10582

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67343 AN: 68028

Other (OTH) AF: 0.912 AC: 1927 AN: 2112

Alfa AF: 0.938 Hom.: 18595

Bravo AF: 0.895

Asia WGS AF: 0.881 AC: 3063 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	0.26
DANN	Benign	0.71
PhyloP100		-0.89

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: rs4969017;

hg19: chr17-71177788;