chr2-1546537-T-A

Variant names:

• chr2-1546537-T-A
• rs6705087
• NR_198951.1:n.2951A>T

Variant summary

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

The NR_198951.1(LALTOP):​n.2951A>T variant causes a non coding transcript exon 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: LALTOP NR_198951.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

LALTOP (HGNC:58132):

ENSG00000231482 (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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LALTOP	NR_198951.1	n.2951A>T		non_coding_transcript_exon_variant	Exon 4 of 4
LALTOP	NR_198948.1	n.3395+7A>T		splice_region_variant, intron_variant	Intron 5 of 6
LALTOP	NR_198949.1	n.3395+7A>T		splice_region_variant, intron_variant	Intron 5 of 6
LALTOP	NR_198950.1	n.3046+7A>T		splice_region_variant, intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231482	ENST00000650512.1	n.547+33664A>T		intron_variant	Intron 1 of 3
ENSG00000228613	ENST00000816433.1	n.520+7A>T		splice_region_variant, intron_variant	Intron 3 of 3
ENSG00000228613	ENST00000816434.1	n.654+7A>T		splice_region_variant, intron_variant	Intron 2 of 2
ENSG00000228613	ENST00000438247.1	n.*128A>T		downstream_gene_variant		4

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	-0.93
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6705087; hg19: chr2-1550309;