rs9321765

Variant names:

• chr6-140274607-T-C
• rs9321765
• ENST00000683950.1:n.202-40223T>C

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.202-40223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,754 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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.202-40223T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28821 AN: 151636 Hom.: 3007 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.190 AC: 28838 AN: 151754 Hom.: 3008 Cov.: 32 AF XY: 0.190 AC XY: 14107 AN XY: 74180

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.188

Alfa AF: 0.189 Hom.: 364

Bravo AF: 0.187

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321765; hg19: chr6-140595744;