14-53761799-T-C

Variant names:

• chr14-53761799-T-C
• rs1958654
• ENST00000418927.3:n.743+7002A>G

Variant summary

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

The ENST00000418927.3(LINC02331):​n.743+7002A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,062 control chromosomes in the GnomAD database, including 59,850 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 0.89 (59850 hom., cov: 32)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 7 publications found

Genes affected

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

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

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.668+7002A>G		intron_variant	Intron 5 of 6
LINC02331	NR_184213.1	n.668+7002A>G		intron_variant	Intron 5 of 6
LINC02331	NR_184214.1	n.679+7002A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.743+7002A>G		intron_variant	Intron 4 of 5	5
DDHD1-DT	ENST00000648066.2	n.951-3859T>C		intron_variant	Intron 6 of 9
DDHD1-DT	ENST00000728781.1	n.176+74425T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134702 AN: 151944 Hom.: 59787 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.887 AC: 134824 AN: 152062 Hom.: 59850 Cov.: 32 AF XY: 0.887 AC XY: 65883 AN XY: 74318

African (AFR) AF: 0.909 AC: 37768 AN: 41540

American (AMR) AF: 0.904 AC: 13808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3148 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5186

South Asian (SAS) AF: 0.932 AC: 4497 AN: 4826

European-Finnish (FIN) AF: 0.837 AC: 8867 AN: 10594

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58527 AN: 67858

Other (OTH) AF: 0.904 AC: 1909 AN: 2112

Alfa AF: 0.880 Hom.: 132440

Bravo AF: 0.895

Asia WGS AF: 0.963 AC: 3348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.38
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1958654; hg19: chr14-54228517;