6-16940287-T-C

Position:

• chr6-16940287-T-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

(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/exons	MANE	Protein	UniProt
		n.16940287T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287347	ENST00000654689.1	n.183-242A>G		intron_variant

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;