6-150552630-C-T

Position:

• chr6-150552630-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 0.564 in 149,576 control chromosomes in the GnomAD database, including 24,078 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 0.56 (24078 hom., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150552630C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.564 AC: 84264 AN: 149458 Hom.: 24074 Cov.: 24

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.564 AC: 84300 AN: 149576 Hom.: 24078 Cov.: 24 AF XY: 0.567 AC XY: 41287 AN XY: 72834

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.509

Alfa AF: 0.564 Hom.: 46684

Bravo AF: 0.543

Asia WGS AF: 0.547 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7740233; hg19: chr6-150873766;