6-367109-C-G

Variant names:

• chr6-367109-C-G
• rs2671415
• ENST00000793853.1:n.395-5713G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000793853.1(ENSG00000303358):​n.395-5713G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000303358 ENST00000793853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 2 publications found

Genes affected

ENSG00000303358 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAd4 at 54 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793853.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303358	ENST00000793853.1		n.395-5713G>C		intron	N/A

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.196 AC: 7669 AN: 39192

American (AMR) AF: 0.166 AC: 2430 AN: 14676

Ashkenazi Jewish (ASJ) AF: 0.0857 AC: 294 AN: 3430

East Asian (EAS) AF: 0.310 AC: 1535 AN: 4946

South Asian (SAS) AF: 0.143 AC: 657 AN: 4606

European-Finnish (FIN) AF: 0.0898 AC: 928 AN: 10330

Middle Eastern (MID) AF: 0.0833 AC: 24 AN: 288

European-Non Finnish (NFE) AF: 0.0538 AC: 3605 AN: 67008

Other (OTH) AF: 0.110 AC: 226 AN: 2052

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0264 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.37
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs2671415; hg19: chr6-367109;