6-168356431-C-T

Variant names:

• chr6-168356431-C-T
• rs6915443

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;