6-63155077-T-C

Variant names:

• chr6-63155077-T-C
• rs6454050

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 0.172 in 152,184 control chromosomes in the GnomAD database, including 2,839 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 0.17 (2839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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 = 0.302 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: 0.172 AC: 26223 AN: 152066 Hom.: 2836 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.172 AC: 26248 AN: 152184 Hom.: 2839 Cov.: 32 AF XY: 0.169 AC XY: 12564 AN XY: 74394

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.0646

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.170

Alfa AF: 0.109 Hom.: 300

Bravo AF: 0.189

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6454050; hg19: chr6-63864982;