6-16940287-T-C

Variant names:

• chr6-16940287-T-C
• rs6459492
• ENST00000654689.1:n.183-242A>G

Variant summary

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

The ENST00000654689.1(ENSG00000287347):​n.183-242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 151,980 control chromosomes in the GnomAD database, including 64,674 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 0.92 (64674 hom., cov: 28)
• Consequence: ENSG00000287347 ENST00000654689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

ENSG00000287347 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 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
ENSG00000287347	ENST00000654689.1	n.183-242A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139907 AN: 151862 Hom.: 64612 Cov.: 28

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.921 AC: 140028 AN: 151980 Hom.: 64674 Cov.: 28 AF XY: 0.921 AC XY: 68418 AN XY: 74268

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.918

Alfa AF: 0.906 Hom.: 62587

Bravo AF: 0.927

Asia WGS AF: 0.886 AC: 3080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
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: rs6459492; hg19: chr6-16940518;