rs2785980

Variant names:

• chr1-219527177-T-C
• rs2785980
• ENST00000811290.1:n.60+22673A>G

Variant summary

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

The ENST00000811290.1(LYPLAL1-AS1):​n.60+22673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,120 control chromosomes in the GnomAD database, including 6,651 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 0.28 (6651 hom., cov: 32)
• Consequence: LYPLAL1-AS1 ENST00000811290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 31 publications found

Genes affected

LYPLAL1-AS1 (HGNC:54054): (LYPLAL1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYPLAL1-AS1	NR_135822.1	n.134+30014A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-AS1	ENST00000811290.1	n.60+22673A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42332 AN: 152002 Hom.: 6647 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.278 AC: 42352 AN: 152120 Hom.: 6651 Cov.: 32 AF XY: 0.282 AC XY: 20968 AN XY: 74362

African (AFR) AF: 0.140 AC: 5808 AN: 41522

American (AMR) AF: 0.420 AC: 6417 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5162

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3568 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22230 AN: 67966

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.310 Hom.: 19762

Bravo AF: 0.282

Asia WGS AF: 0.261 AC: 906 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2785980; hg19: chr1-219700519; COSMIC: COSV60029335;