rs6705087

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-1546537-T-A
• chr2-1546537-T-C
• chr2-1546537-T-G

Variant summary

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

The NR_198948.1(LALTOP):​n.3395+7A>T variant causes a splice region, 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: LALTOP NR_198948.1 splice_region, intron
• 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_198948.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LALTOP	NR_198951.1		n.2951A>T		non_coding_transcript_exon	Exon 4 of 4
	LALTOP	NR_198948.1		n.3395+7A>T		splice_region intron	N/A
	LALTOP	NR_198949.1		n.3395+7A>T		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231482	ENST00000650512.1		n.547+33664A>T		intron	N/A
	LALTOP	ENST00000816433.1		n.520+7A>T		splice_region intron	N/A
	LALTOP	ENST00000816434.1		n.654+7A>T		splice_region intron	N/A

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 v4.9

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;