6-411954-C-T

Variant names:

• chr6-411954-C-T
• rs11242865

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;