6-31188026-C-T

Variant names:

• chr6-31188026-C-T
• rs9405015
• ENST00000755443.1:n.183-1756G>A

Variant summary

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

The ENST00000755443.1(ENSG00000272501):​n.183-1756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 151,708 control chromosomes in the GnomAD database, including 105 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 0.024 (105 hom., cov: 31)
• Consequence: ENSG00000272501 ENST00000755443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 9 publications found

Genes affected

ENSG00000272501 (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 (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755443.1. 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
	ENSG00000272501	ENST00000755443.1		n.183-1756G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3647 AN: 151616 Hom.: 103 Cov.: 31

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0241 AC: 3658 AN: 151708 Hom.: 105 Cov.: 31 AF XY: 0.0262 AC XY: 1944 AN XY: 74098

African (AFR) AF: 0.00566 AC: 234 AN: 41350

American (AMR) AF: 0.0437 AC: 666 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0211 AC: 73 AN: 3466

East Asian (EAS) AF: 0.168 AC: 869 AN: 5158

South Asian (SAS) AF: 0.0371 AC: 178 AN: 4796

European-Finnish (FIN) AF: 0.0284 AC: 296 AN: 10422

Middle Eastern (MID) AF: 0.0104 AC: 3 AN: 288

European-Non Finnish (NFE) AF: 0.0187 AC: 1272 AN: 67964

Other (OTH) AF: 0.0313 AC: 66 AN: 2106

Alfa AF: 0.0203 Hom.: 129

Bravo AF: 0.0233

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		-0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9405015;

hg19: chr6-31155803;