rs1342371

Variant names:

• chr6-44772212-C-G
• rs1342371
• ENST00000671451.2:n.195+44133C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-44772212-C-G
• chr6-44772212-C-T

Variant summary

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

The ENST00000671451.2(ENSG00000286417):​n.195+44133C>G 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: 0.283
• Publications: 0 publications found

Genes affected

ENSG00000286417 (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=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929770	XR_007059596.1	n.252-307C>G		intron_variant	Intron 1 of 2
LOC101929770	XR_007059597.1	n.251+40844C>G		intron_variant	Intron 1 of 1
LOC101929770	XR_007059598.1	n.144+44133C>G		intron_variant	Intron 1 of 1
LOC101929770	XR_926855.3	n.145-307C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286417	ENST00000671451.2	n.195+44133C>G		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.174-307C>G		intron_variant	Intron 1 of 3
ENSG00000286417	ENST00000811307.1	n.188-307C>G		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	-0.83
CADD	Benign	3.6
DANN	Benign	0.65
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1342371; hg19: chr6-44739949;