2-64396599-T-G

Position:

• chr2-64396599-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441630.1(LGALSL-DT):​n.278-934A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALSL-DT	XR_002959392.2	n.454-934A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALSL-DT	ENST00000441630.1	n.278-934A>C		intron_variant, non_coding_transcript_variant		3
LGALSL-DT	ENST00000647983.1	n.378-934A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.283

Alfa AF: 0.285 Hom.: 8536

Bravo AF: 0.266

Asia WGS AF: 0.175 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496112; hg19: chr2-64623733;