rs9376506

Variant names:

• chr6-140252173-C-T
• rs9376506
• ENST00000826362.1:n.88G>A

Variant summary

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

The ENST00000826362.1(ENSG00000307447):​n.88G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,146 control chromosomes in the GnomAD database, including 2,810 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 0.18 (2810 hom., cov: 32)
• Consequence: ENSG00000307447 ENST00000826362.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 1 publications found

Genes affected

ENSG00000307447 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307447	ENST00000826362.1	n.88G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000288714	ENST00000683950.1	n.202-62657C>T		intron_variant	Intron 1 of 1
ENSG00000288714	ENST00000825769.1	n.176-62657C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27148 AN: 152028 Hom.: 2811 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.179 AC: 27159 AN: 152146 Hom.: 2810 Cov.: 32 AF XY: 0.179 AC XY: 13301 AN XY: 74382

African (AFR) AF: 0.0848 AC: 3520 AN: 41528

American (AMR) AF: 0.205 AC: 3139 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2104 AN: 5154

South Asian (SAS) AF: 0.184 AC: 886 AN: 4826

European-Finnish (FIN) AF: 0.219 AC: 2317 AN: 10580

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13779 AN: 67986

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.184 Hom.: 330

Bravo AF: 0.175

Asia WGS AF: 0.284 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.87
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs9376506; hg19: chr6-140573310; COSMIC: COSV65388649;