ENST00000441630.1:n.278-934A>C

Variant names:

• chr2-64396599-T-G
• rs10496112
• ENST00000441630.1:n.278-934A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441630.1(LGALSL-DT):​n.278-934A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,064 control chromosomes in the GnomAD database, including 5,683 homozygotes. 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: 𝑓 0.27 (5683 hom., cov: 32)
• Consequence: LGALSL-DT ENST00000441630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 4 publications found

Genes affected

LGALSL-DT (HGNC:53951): (LGALSL divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441630.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALSL-DT	ENST00000441630.1	TSL:3	n.278-934A>C		intron	N/A
	LGALSL-DT	ENST00000647983.1		n.378-934A>C		intron	N/A
	LGALSL-DT	ENST00000811778.1		n.156-934A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40653 AN: 151946 Hom.: 5672 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.268 AC: 40704 AN: 152064 Hom.: 5683 Cov.: 32 AF XY: 0.264 AC XY: 19613 AN XY: 74332

African (AFR) AF: 0.218 AC: 9022 AN: 41470

American (AMR) AF: 0.286 AC: 4373 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 987 AN: 3468

East Asian (EAS) AF: 0.0927 AC: 480 AN: 5180

South Asian (SAS) AF: 0.200 AC: 962 AN: 4814

European-Finnish (FIN) AF: 0.291 AC: 3075 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20739 AN: 67966

Other (OTH) AF: 0.283 AC: 596 AN: 2106

Alfa AF: 0.283 Hom.: 18159

Bravo AF: 0.266

Asia WGS AF: 0.175 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10496112; hg19: chr2-64623733;