rs10805650

Variant names:

• chr5-17771678-G-A
• rs10805650
• ENST00000790440.1:n.272G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-17771678-G-A
• chr5-17771678-G-T

Variant summary

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

The ENST00000790440.1(LINC02223):​n.272G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,934 control chromosomes in the GnomAD database, including 29,950 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 0.62 (29950 hom., cov: 31)
• Consequence: LINC02223 ENST00000790440.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

Genes affected

LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

LOC105374666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374666	XR_001742615.2	n.407G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105374666	XR_925809.3	n.305+2694G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000790440.1	n.272G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02223	ENST00000511596.5	n.195+2694G>A		intron_variant	Intron 2 of 4	5
LINC02223	ENST00000648234.1	n.451+2694G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94254 AN: 151816 Hom.: 29939 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.621 AC: 94300 AN: 151934 Hom.: 29950 Cov.: 31 AF XY: 0.619 AC XY: 45971 AN XY: 74232

African (AFR) AF: 0.474 AC: 19610 AN: 41404

American (AMR) AF: 0.609 AC: 9291 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2877 AN: 5158

South Asian (SAS) AF: 0.634 AC: 3050 AN: 4812

European-Finnish (FIN) AF: 0.695 AC: 7327 AN: 10546

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47376 AN: 67968

Other (OTH) AF: 0.656 AC: 1386 AN: 2114

Alfa AF: 0.645 Hom.: 5275

Bravo AF: 0.609

Asia WGS AF: 0.574 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.77
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10805650; hg19: chr5-17771787;