6-156178397-C-T

Variant names:

• chr6-156178397-C-T
• rs9384428
• ENST00000663591.1:n.398+73923G>A

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.398+73923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,974 control chromosomes in the GnomAD database, including 39,746 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 0.72 (39746 hom., cov: 31)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 4 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663591.1. 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
	ENSG00000287092	ENST00000663591.1		n.398+73923G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108934 AN: 151858 Hom.: 39709 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.717 AC: 109019 AN: 151974 Hom.: 39746 Cov.: 31 AF XY: 0.719 AC XY: 53411 AN XY: 74284

African (AFR) AF: 0.830 AC: 34387 AN: 41424

American (AMR) AF: 0.550 AC: 8403 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2109 AN: 3468

East Asian (EAS) AF: 0.691 AC: 3575 AN: 5170

South Asian (SAS) AF: 0.684 AC: 3294 AN: 4816

European-Finnish (FIN) AF: 0.765 AC: 8068 AN: 10550

Middle Eastern (MID) AF: 0.672 AC: 195 AN: 290

European-Non Finnish (NFE) AF: 0.691 AC: 46977 AN: 67958

Other (OTH) AF: 0.688 AC: 1449 AN: 2106

Alfa AF: 0.699 Hom.: 18588

Bravo AF: 0.705

Asia WGS AF: 0.674 AC: 2342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.91
DANN	Benign	0.57
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs9384428; hg19: chr6-156499531; COSMIC: COSV69431237;