6-44730971-G-C

Variant names:

• chr6-44730971-G-C
• rs227849
• ENST00000671451.2:n.195+2892G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000671451.2(ENSG00000286417):​n.195+2892G>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: 33)
• Consequence: ENSG00000286417 ENST00000671451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 13 publications found

Genes affected

ENSG00000286417 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929770	XR_007059598.1	n.144+2892G>C		intron_variant	Intron 1 of 1
LOC101929770	XR_926855.3	n.144+2892G>C		intron_variant	Intron 1 of 2
LOC101929770	XR_007059596.1	n.-147G>C		upstream_gene_variant
LOC101929770	XR_007059597.1	n.-147G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286417	ENST00000671451.2	n.195+2892G>C		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.173+2892G>C		intron_variant	Intron 1 of 3
ENSG00000286417	ENST00000811307.1	n.187+2892G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs227849; hg19: chr6-44698708;