rs9376506

Variant names:

• chr6-140252173-C-T
• rs9376506
• ENST00000683950.1:n.202-62657C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000683950.1(ENSG00000288714):​n.202-62657C>T variant causes a intron 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: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000288714	ENST00000683950.1	n.202-62657C>T		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.179

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

Splicing

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

Publications

LitVar

Other links and lift over

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