6-140528565-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000288714	ENST00000825769.1	n.371-10668T>G		intron_variant	Intron 3 of 7

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

African (AFR) AF: 0.176 AC: 7294 AN: 41516

American (AMR) AF: 0.475 AC: 7245 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1742 AN: 3466

East Asian (EAS) AF: 0.528 AC: 2722 AN: 5152

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 5004 AN: 10546

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35003 AN: 67906

Other (OTH) AF: 0.484 AC: 1019 AN: 2106

Alfa AF: 0.469 Hom.: 34409

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
PhyloP100		0.11

Splicing

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

Other links and lift over

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