rs2040450

Positions:

• chr6-30366562-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 0.107 in 150,302 control chromosomes in the GnomAD database, including 1,071 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 0.11 (1071 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

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 (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16145 AN: 150194 Hom.: 1070 Cov.: 30

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.107 AC: 16144 AN: 150302 Hom.: 1071 Cov.: 30 AF XY: 0.106 AC XY: 7768 AN XY: 73248

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0898

Gnomad4 EAS AF: 0.0458

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.127

Alfa AF: 0.134 Hom.: 1020

Bravo AF: 0.110

Asia WGS AF: 0.0650 AC: 227 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	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040450; hg19: chr6-30334339;