chr6-63155077-T-C

Variant names:

• chr6-63155077-T-C
• rs6454050

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.306 AC: 12704 AN: 41490

American (AMR) AF: 0.194 AC: 2971 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.188 AC: 972 AN: 5170

South Asian (SAS) AF: 0.0649 AC: 313 AN: 4824

European-Finnish (FIN) AF: 0.0646 AC: 685 AN: 10606

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7700 AN: 68010

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.114 Hom.: 341

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
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs6454050; hg19: chr6-63864982;