6-43837088-A-C

Variant names:

• chr6-43837088-A-C
• rs2396084
• ENST00000637813.1:n.366-5423A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000637813.1(ENSG00000283573):​n.366-5423A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ENSG00000283573 ENST00000637813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 10 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375069	XR_001744130.1	n.676-77T>G		intron_variant	Intron 2 of 2
LOC105375070	XR_007059588.1	n.193-5423A>C		intron_variant	Intron 1 of 2
LOC105375070	XR_007059589.1	n.193-5423A>C		intron_variant	Intron 1 of 2
LOC105375069	XR_007059590.1	n.393-77T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000637813.1	n.366-5423A>C		intron_variant	Intron 2 of 2	4
ENSG00000283573	ENST00000719551.1	n.193-5423A>C		intron_variant	Intron 1 of 2
ENSG00000294041	ENST00000720677.1	n.332+114A>C		intron_variant	Intron 1 of 1
ENSG00000294041	ENST00000720678.1	n.325+114A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2396084; hg19: chr6-43804825;