6-140169327-C-T

Position:

• chr6-140169327-C-T

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.201+20637C>T variant causes a intron, non coding transcript 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: ENST00000683950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000683950.1	n.201+20637C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.177

Alfa AF: 0.183 Hom.: 332

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321764; hg19: chr6-140490464;