17-73180005-G-T

Variant names:

• chr17-73180005-G-T
• rs6501603
• ENST00000580671.1:n.313-7834G>T

Variant summary

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

The ENST00000580671.1(ENSG00000264860):​n.313-7834G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,954 control chromosomes in the GnomAD database, including 18,227 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 0.49 (18227 hom., cov: 31)
• Consequence: ENSG00000264860 ENST00000580671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 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.313-7834G>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74071 AN: 151836 Hom.: 18212 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.488 AC: 74138 AN: 151954 Hom.: 18227 Cov.: 31 AF XY: 0.488 AC XY: 36218 AN XY: 74272

African (AFR) AF: 0.441 AC: 18275 AN: 41422

American (AMR) AF: 0.484 AC: 7384 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1473 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3143 AN: 5162

South Asian (SAS) AF: 0.492 AC: 2372 AN: 4820

European-Finnish (FIN) AF: 0.489 AC: 5153 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34707 AN: 67970

Other (OTH) AF: 0.494 AC: 1037 AN: 2098

Alfa AF: 0.459 Hom.: 4560

Bravo AF: 0.490

Asia WGS AF: 0.541 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6501603; hg19: chr17-71176144;