6-411954-C-T

Position:

• chr6-411954-C-T

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 0.176 in 152,098 control chromosomes in the GnomAD database, including 2,526 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 (2526 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.411954C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26777 AN: 151980 Hom.: 2527 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.176 AC: 26787 AN: 152098 Hom.: 2526 Cov.: 32 AF XY: 0.173 AC XY: 12897 AN XY: 74360

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.196

Alfa AF: 0.178 Hom.: 1608

Bravo AF: 0.177

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11242865; hg19: chr6-411954;