rs9321765

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683950.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288714	ENST00000683950.1		n.202-40223T>C		intron	N/A
	ENSG00000288714	ENST00000825769.1		n.176-40223T>C		intron	N/A

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

African (AFR) AF: 0.123 AC: 5108 AN: 41488

American (AMR) AF: 0.211 AC: 3214 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3464

East Asian (EAS) AF: 0.409 AC: 2109 AN: 5154

South Asian (SAS) AF: 0.184 AC: 886 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2319 AN: 10586

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13754 AN: 67708

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.202 Hom.: 4219

Bravo AF: 0.187

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9321765;

hg19: chr6-140595744;