ENST00000763589.1:n.133-18535G>A

Variant names:

• chr6-54721839-C-T
• rs9474972
• ENST00000763589.1:n.133-18535G>A

Variant summary

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

The ENST00000763589.1(ENSG00000299445):​n.133-18535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,930 control chromosomes in the GnomAD database, including 18,462 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 0.48 (18462 hom., cov: 31)
• Consequence: ENSG00000299445 ENST00000763589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 6 publications found

Genes affected

ENSG00000299445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763589.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299445	ENST00000763589.1		n.133-18535G>A		intron	N/A
	ENSG00000299445	ENST00000763590.1		n.88-18535G>A		intron	N/A
	ENSG00000299445	ENST00000763591.1		n.70-66162G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72539 AN: 151812 Hom.: 18453 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.478 AC: 72575 AN: 151930 Hom.: 18462 Cov.: 31 AF XY: 0.476 AC XY: 35339 AN XY: 74230

African (AFR) AF: 0.335 AC: 13865 AN: 41440

American (AMR) AF: 0.382 AC: 5823 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1186 AN: 5146

South Asian (SAS) AF: 0.542 AC: 2613 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6099 AN: 10554

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39242 AN: 67950

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.523 Hom.: 11961

Bravo AF: 0.452

Asia WGS AF: 0.392 AC: 1362 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9474972; hg19: chr6-54586637; COSMIC: COSV107166895;