6-367109-C-G

Variant names:

• chr6-367109-C-G
• rs2671415

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 0.118 in 147,434 control chromosomes in the GnomAD database, including 54 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 0.12 (54 hom., cov: 62)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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: 0.118 AC: 17395 AN: 147326 Hom.: 54 Cov.: 62

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0475

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0857

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.0806

Gnomad NFE AF: 0.0538

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.118 AC: 17411 AN: 147434 Hom.: 54 Cov.: 62 AF XY: 0.123 AC XY: 8829 AN XY: 71924

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0857

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0538

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0264 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2671415; hg19: chr6-367109;