rs864754

Variant names:

• chr22-27192801-T-A
• rs864754
• ENST00000805083.1:n.354+20212A>T

Your query was ambiguous. Multiple possible variants found:

• chr22-27192801-T-A
• chr22-27192801-T-C

Variant summary

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

The ENST00000805083.1(LINC01638):​n.354+20212A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,166 control chromosomes in the GnomAD database, including 8,298 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 0.33 (8298 hom., cov: 33)
• Consequence: LINC01638 ENST00000805083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 2 publications found

Genes affected

LINC01638 (HGNC:52425): (long intergenic non-protein coding RNA 1638)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805083.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01638	ENST00000805083.1		n.354+20212A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49479 AN: 152048 Hom.: 8291 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.325 AC: 49508 AN: 152166 Hom.: 8298 Cov.: 33 AF XY: 0.320 AC XY: 23814 AN XY: 74388

African (AFR) AF: 0.370 AC: 15375 AN: 41500

American (AMR) AF: 0.384 AC: 5865 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5174

South Asian (SAS) AF: 0.340 AC: 1644 AN: 4830

European-Finnish (FIN) AF: 0.188 AC: 1995 AN: 10592

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20899 AN: 68000

Other (OTH) AF: 0.377 AC: 796 AN: 2114

Alfa AF: 0.310 Hom.: 951

Bravo AF: 0.345

Asia WGS AF: 0.303 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.023
DANN	Benign	0.52
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs864754; hg19: chr22-27588763;