rs2987775

Variant names:

• chr1-60622054-A-G
• rs2987775
• ENST00000439156.2:n.336+17957T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-60622054-A-G
• chr1-60622054-A-T

Variant summary

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

The ENST00000439156.2(LINC01748):​n.336+17957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,002 control chromosomes in the GnomAD database, including 32,044 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 0.63 (32044 hom., cov: 31)
• Consequence: LINC01748 ENST00000439156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 3 publications found

Genes affected

LINC01748 (HGNC:52535): (long intergenic non-protein coding RNA 1748)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01748	NR_146508.1	n.189+443T>C		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01748	ENST00000439156.2	n.336+17957T>C		intron_variant	Intron 2 of 7	5
LINC01748	ENST00000634836.1	n.189+443T>C		intron_variant	Intron 1 of 7	5
LINC01748	ENST00000635048.2	n.49+443T>C		intron_variant	Intron 1 of 8	5

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96276 AN: 151884 Hom.: 31975 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.634 AC: 96403 AN: 152002 Hom.: 32044 Cov.: 31 AF XY: 0.634 AC XY: 47053 AN XY: 74260

African (AFR) AF: 0.825 AC: 34236 AN: 41482

American (AMR) AF: 0.633 AC: 9658 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3720 AN: 5166

South Asian (SAS) AF: 0.784 AC: 3774 AN: 4816

European-Finnish (FIN) AF: 0.485 AC: 5120 AN: 10552

Middle Eastern (MID) AF: 0.572 AC: 166 AN: 290

European-Non Finnish (NFE) AF: 0.531 AC: 36105 AN: 67950

Other (OTH) AF: 0.625 AC: 1317 AN: 2106

Alfa AF: 0.571 Hom.: 3636

Bravo AF: 0.649

Asia WGS AF: 0.767 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2987775; hg19: chr1-61087726;