14-53703022-G-A

Variant names:

• chr14-53703022-G-A
• rs210357
• ENST00000728989.1:n.994C>T

Variant summary

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

The ENST00000728989.1(LINC02331):​n.994C>T 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 0.114 in 152,170 control chromosomes in the GnomAD database, including 1,251 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 0.11 (1251 hom., cov: 32)
• Consequence: LINC02331 ENST00000728989.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 5 publications found

Genes affected

LINC02331 (HGNC:53251): (long intergenic non-protein coding RNA 2331)

DDHD1-DT (HGNC:55441): (DDHD1 divergent transcript)

LOC105370504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184213.1	n.900C>T		non_coding_transcript_exon_variant	Exon 7 of 7
LINC02331	NR_184212.1	n.768-16414C>T		intron_variant	Intron 6 of 6
LINC02331	NR_184214.1	n.779-16414C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000728989.1	n.994C>T		non_coding_transcript_exon_variant	Exon 6 of 7
LINC02331	ENST00000728990.1	n.1181C>T		non_coding_transcript_exon_variant	Exon 7 of 7
LINC02331	ENST00000728991.1	n.978C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17336 AN: 152052 Hom.: 1245 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.114 AC: 17376 AN: 152170 Hom.: 1251 Cov.: 32 AF XY: 0.115 AC XY: 8568 AN XY: 74390

African (AFR) AF: 0.185 AC: 7666 AN: 41486

American (AMR) AF: 0.124 AC: 1898 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5176

South Asian (SAS) AF: 0.133 AC: 641 AN: 4820

European-Finnish (FIN) AF: 0.0380 AC: 402 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5118 AN: 68018

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0740 Hom.: 287

Bravo AF: 0.122

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.78
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs210357; hg19: chr14-54169740;