rs2223163

Variant names:

• chr21-14855657-G-A
• rs2223163
• ENST00000412426.5:n.191+1885C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-14855657-G-A
• chr21-14855657-G-T

Variant summary

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

The ENST00000418954.2(LINC02246):​n.256+1885C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,018 control chromosomes in the GnomAD database, including 31,721 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 (31721 hom., cov: 32)
• Consequence: LINC02246 ENST00000418954.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

Genes affected

LINC02246 (HGNC:53135): (adipocyte associated metabolic related lncRNA 1)

ENSG00000235609 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASMER1	NR_146322.1	n.665+1885C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02246	ENST00000412426.5	n.191+1885C>T		intron_variant	Intron 2 of 3	5
LINC02246	ENST00000418954.2	n.256+1885C>T		intron_variant	Intron 2 of 2	2
ENSG00000235609	ENST00000432230.6	n.254+1885C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95488 AN: 151900 Hom.: 31714 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.628 AC: 95539 AN: 152018 Hom.: 31721 Cov.: 32 AF XY: 0.625 AC XY: 46459 AN XY: 74306

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.655

Alfa AF: 0.585 Hom.: 1989

Bravo AF: 0.611

Asia WGS AF: 0.437 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2223163; hg19: chr21-16227978;