6-168356431-C-T

Position:

• chr6-168356431-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 0.129 in 152,250 control chromosomes in the GnomAD database, including 1,711 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 0.13 (1711 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19601 AN: 152132 Hom.: 1706 Cov.: 34

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.129 AC: 19624 AN: 152250 Hom.: 1711 Cov.: 34 AF XY: 0.128 AC XY: 9560 AN XY: 74432

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0625 Hom.: 79

Bravo AF: 0.128

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6915443; hg19: chr6-168757111;