6-37059456-C-T

Variant names:

• chr6-37059456-C-T
• rs9366927
• ENST00000739933.1:n.296-34615G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000739933.1(ENSG00000296499):​n.296-34615G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,874 control chromosomes in the GnomAD database, including 26,460 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 0.58 (26460 hom., cov: 30)
• Consequence: ENSG00000296499 ENST00000739933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 9 publications found

Genes affected

ENSG00000296499 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739933.1. 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
	ENSG00000296499	ENST00000739933.1		n.296-34615G>A		intron	N/A
	ENSG00000296499	ENST00000739934.1		n.328-17077G>A		intron	N/A
	ENSG00000296499	ENST00000739935.1		n.134-17077G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88435 AN: 151756 Hom.: 26435 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.583 AC: 88512 AN: 151874 Hom.: 26460 Cov.: 30 AF XY: 0.590 AC XY: 43807 AN XY: 74200

African (AFR) AF: 0.616 AC: 25511 AN: 41408

American (AMR) AF: 0.666 AC: 10152 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3468

East Asian (EAS) AF: 0.893 AC: 4603 AN: 5154

South Asian (SAS) AF: 0.692 AC: 3337 AN: 4822

European-Finnish (FIN) AF: 0.597 AC: 6282 AN: 10516

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35140 AN: 67936

Other (OTH) AF: 0.588 AC: 1243 AN: 2114

Alfa AF: 0.544 Hom.: 7336

Bravo AF: 0.592

Asia WGS AF: 0.751 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	19
DANN	Benign	0.91
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9366927; hg19: chr6-37027232;