6-51000259-C-T

Position:

• chr6-51000259-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 0.502 in 151,940 control chromosomes in the GnomAD database, including 19,412 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 0.50 (19412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76290 AN: 151820 Hom.: 19397 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.502 AC: 76348 AN: 151940 Hom.: 19412 Cov.: 32 AF XY: 0.502 AC XY: 37243 AN XY: 74240

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.463

Alfa AF: 0.503 Hom.: 2434

Bravo AF: 0.504

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283545; hg19: chr6-50967972;