6-140169327-C-T

Variant names:

• chr6-140169327-C-T
• rs9321764
• ENST00000683950.1:n.201+20637C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000683950.1(ENSG00000288714):​n.201+20637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,838 control chromosomes in the GnomAD database, including 2,779 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 (2779 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 1 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=-0.98).
• 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.201+20637C>T		intron_variant	Intron 1 of 1
ENSG00000288714	ENST00000825769.1	n.175+20637C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26894 AN: 151718 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.177 AC: 26908 AN: 151838 Hom.: 2779 Cov.: 32 AF XY: 0.177 AC XY: 13145 AN XY: 74206

African (AFR) AF: 0.0854 AC: 3546 AN: 41512

American (AMR) AF: 0.204 AC: 3108 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3462

East Asian (EAS) AF: 0.410 AC: 2111 AN: 5152

South Asian (SAS) AF: 0.158 AC: 758 AN: 4808

European-Finnish (FIN) AF: 0.219 AC: 2306 AN: 10528

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13682 AN: 67820

Other (OTH) AF: 0.177 AC: 372 AN: 2102

Alfa AF: 0.178 Hom.: 335

Bravo AF: 0.174

Asia WGS AF: 0.270 AC: 932 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.57
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs9321764; hg19: chr6-140490464;