rs2671415

chr6-367109-C-Gchr6-367109-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 0.118 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;