chr21-45260651-G-C

Variant names:

• chr21-45260651-G-C
• rs2838855
• ENST00000638500.2:n.1090+1366G>C

Variant summary

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

The ENST00000638500.2(LINC00334):​n.1090+1366G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,160 control chromosomes in the GnomAD database, including 7,318 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 0.31 (7318 hom., cov: 33)
• Consequence: LINC00334 ENST00000638500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 9 publications found

Genes affected

LINC00334 (HGNC:16425): (long intergenic non-protein coding RNA 334)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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
LINC00334	ENST00000638500.2	n.1090+1366G>C		intron_variant	Intron 3 of 3	5
LINC00334	ENST00000660971.1	n.1004+1366G>C		intron_variant	Intron 2 of 2
LINC00334	ENST00000665973.1	n.1080+1366G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46485 AN: 152042 Hom.: 7309 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.306 AC: 46517 AN: 152160 Hom.: 7318 Cov.: 33 AF XY: 0.309 AC XY: 23009 AN XY: 74378

African (AFR) AF: 0.308 AC: 12804 AN: 41512

American (AMR) AF: 0.275 AC: 4211 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1123 AN: 3472

East Asian (EAS) AF: 0.447 AC: 2311 AN: 5174

South Asian (SAS) AF: 0.431 AC: 2076 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10572

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

European-Non Finnish (NFE) AF: 0.295 AC: 20063 AN: 68004

Other (OTH) AF: 0.315 AC: 666 AN: 2114

Alfa AF: 0.290 Hom.: 808

Bravo AF: 0.304

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.37
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2838855; hg19: chr21-46680566;