rs6928289

Variant names:

• chr6-137352165-G-A
• rs6928289
• ENST00000719209.1:n.215-17409C>T

Variant summary

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

The ENST00000719209.1(ENSG00000293815):​n.215-17409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,080 control chromosomes in the GnomAD database, including 17,050 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 0.47 (17050 hom., cov: 33)
• Consequence: ENSG00000293815 ENST00000719209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 4 publications found

Genes affected

ENSG00000293815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719209.1. 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
	ENSG00000293815	ENST00000719209.1		n.215-17409C>T		intron	N/A
	ENSG00000293815	ENST00000719210.1		n.159+5575C>T		intron	N/A
	ENSG00000293844	ENST00000719379.1		n.59+160G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70811 AN: 151962 Hom.: 17045 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.466 AC: 70856 AN: 152080 Hom.: 17050 Cov.: 33 AF XY: 0.470 AC XY: 34920 AN XY: 74328

African (AFR) AF: 0.549 AC: 22764 AN: 41468

American (AMR) AF: 0.439 AC: 6708 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1765 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3820 AN: 5166

South Asian (SAS) AF: 0.565 AC: 2718 AN: 4808

European-Finnish (FIN) AF: 0.405 AC: 4282 AN: 10572

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27413 AN: 67984

Other (OTH) AF: 0.469 AC: 991 AN: 2112

Alfa AF: 0.459 Hom.: 13864

Bravo AF: 0.471

Asia WGS AF: 0.602 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs6928289; hg19: chr6-137673302; COSMIC: COSV60284305;