6-30366562-C-T

Variant names:

• chr6-30366562-C-T
• rs2040450

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 0.107 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0479 AC: 1951 AN: 40758

American (AMR) AF: 0.153 AC: 2299 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.0898 AC: 311 AN: 3464

East Asian (EAS) AF: 0.0458 AC: 235 AN: 5134

South Asian (SAS) AF: 0.0786 AC: 374 AN: 4758

European-Finnish (FIN) AF: 0.123 AC: 1236 AN: 10080

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9326 AN: 67774

Other (OTH) AF: 0.127 AC: 265 AN: 2082

Alfa AF: 0.127 Hom.: 3530

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
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs2040450; hg19: chr6-30334339;