16-25091199-T-C

Variant names:

• chr16-25091199-T-C
• rs874562
• ENST00000563962.6:n.436-4476A>G

Variant summary

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

The ENST00000563962.6(LCMT1-AS1):​n.436-4476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,180 control chromosomes in the GnomAD database, including 23,479 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 0.55 (23479 hom., cov: 34)
• Consequence: LCMT1-AS1 ENST00000563962.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 6 publications found

Genes affected

LCMT1-AS1 (HGNC:51177): (LCMT1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCMT1-AS1	ENST00000563962.6	n.436-4476A>G		intron_variant	Intron 2 of 2	3
LCMT1-AS1	ENST00000566507.3	n.481-5427A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83247 AN: 152062 Hom.: 23447 Cov.: 34

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.548 AC: 83335 AN: 152180 Hom.: 23479 Cov.: 34 AF XY: 0.543 AC XY: 40401 AN XY: 74376

African (AFR) AF: 0.671 AC: 27864 AN: 41522

American (AMR) AF: 0.497 AC: 7600 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1375 AN: 5188

South Asian (SAS) AF: 0.532 AC: 2563 AN: 4822

European-Finnish (FIN) AF: 0.513 AC: 5431 AN: 10582

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35260 AN: 67986

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.526 Hom.: 12459

Bravo AF: 0.547

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs874562; hg19: chr16-25102520;