10-4035359-A-T

Variant names:

• chr10-4035359-A-T
• rs2645227
• ENST00000656775.1:n.689+3656A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_176060.1(LOC107984195):​n.613+3656A>T 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: 32)
• Consequence: LOC107984195 NR_176060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

ENSG00000227101 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.613+3656A>T		intron_variant	Intron 2 of 9
LOC107984195	NR_176062.1	n.613+3656A>T		intron_variant	Intron 2 of 3
LOC107984195	NR_176063.1	n.867+3656A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227101	ENST00000656775.1	n.689+3656A>T		intron_variant	Intron 2 of 2
ENSG00000227101	ENST00000658139.1	n.568+3656A>T		intron_variant	Intron 2 of 2
ENSG00000227101	ENST00000667089.1	n.627+3656A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2645227; hg19: chr10-4077551;