rs1821383

Variant names:

• chr15-38902852-G-A
• rs1821383

Your query was ambiguous. Multiple possible variants found:

• chr15-38902852-G-A
• chr15-38902852-G-C
• chr15-38902852-G-T

Variant summary

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

The variant allele was found at a frequency of 0.449 in 152,084 control chromosomes in the GnomAD database, including 15,991 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 0.45 (15991 hom., cov: 33)
• Consequence: LOC105370777 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 1 publications found

Genes affected

LOC105370777 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560197.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259345	ENST00000560197.6	TSL:5	n.252-15923C>T		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.255-15923C>T		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.312-15923C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68233 AN: 151966 Hom.: 15970 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.449 AC: 68299 AN: 152084 Hom.: 15991 Cov.: 33 AF XY: 0.452 AC XY: 33604 AN XY: 74334

African (AFR) AF: 0.319 AC: 13218 AN: 41486

American (AMR) AF: 0.553 AC: 8455 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2146 AN: 5160

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4816

European-Finnish (FIN) AF: 0.560 AC: 5916 AN: 10560

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33495 AN: 67970

Other (OTH) AF: 0.443 AC: 937 AN: 2114

Alfa AF: 0.445 Hom.: 3451

Bravo AF: 0.442

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1821383; hg19: chr15-39195053;