6-140528565-T-G

Variant names:

• chr6-140528565-T-G
• rs9376523
• ENST00000684511.1:n.36-10672T>G

Variant summary

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

The ENST00000684511.1(ENSG00000288714):​n.36-10672T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,958 control chromosomes in the GnomAD database, including 15,027 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 0.42 (15027 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000684511.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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	ENST00000684511.1	n.36-10672T>G		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63363 AN: 151840 Hom.: 15027 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.417 AC: 63379 AN: 151958 Hom.: 15027 Cov.: 32 AF XY: 0.418 AC XY: 31053 AN XY: 74254

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.484

Alfa AF: 0.500 Hom.: 26154

Bravo AF: 0.406

Asia WGS AF: 0.547 AC: 1898 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9376523; hg19: chr6-140849702; COSMIC: COSV69429017;