6-150552630-C-T

Variant names:

• chr6-150552630-C-T
• rs7740233

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;