rs1206229

Variant names:

• chrX-137430976-G-A
• rs1206229
• ENST00000786828.1:n.973-17368C>T

Variant summary

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

The ENST00000786828.1(LINC02931):​n.973-17368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 111,610 control chromosomes in the GnomAD database, including 361 homozygotes. There are 2,224 hemizygotes in GnomAD. 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 0.071 (361 hom., 2224 hem., cov: 22)
• Consequence: LINC02931 ENST00000786828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 0 publications found

Genes affected

LINC02931 (HGNC:55853): (long intergenic non-protein coding RNA 2931)

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 = 0.169 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
LINC02931	ENST00000786828.1	n.973-17368C>T		intron_variant	Intron 5 of 5
LINC02931	ENST00000786829.1	n.691-17368C>T		intron_variant	Intron 4 of 4
LINC02931	ENST00000786830.1	n.997-17368C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 7890 AN: 111555 Hom.: 357 Cov.: 22

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0316

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0709 AC: 7910 AN: 111610 Hom.: 361 Cov.: 22 AF XY: 0.0657 AC XY: 2224 AN XY: 33834

African (AFR) AF: 0.173 AC: 5284 AN: 30563

American (AMR) AF: 0.0331 AC: 351 AN: 10610

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 256 AN: 2643

East Asian (EAS) AF: 0.130 AC: 456 AN: 3508

South Asian (SAS) AF: 0.0317 AC: 84 AN: 2651

European-Finnish (FIN) AF: 0.0140 AC: 85 AN: 6052

Middle Eastern (MID) AF: 0.0275 AC: 6 AN: 218

European-Non Finnish (NFE) AF: 0.0244 AC: 1298 AN: 53141

Other (OTH) AF: 0.0584 AC: 90 AN: 1540

Alfa AF: 0.0506 Hom.: 260

Bravo AF: 0.0790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.034
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1206229; hg19: chrX-136513135;