14-22581859-C-T

Variant names:

• chr14-22581859-C-T
• rs8005354
• NM_001344.4:c.212-6626G>A

Variant summary

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

The NM_001344.4(DAD1):​c.212-6626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,718 control chromosomes in the GnomAD database, including 38,749 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 0.70 (38749 hom., cov: 29)
• Consequence: DAD1 NM_001344.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 5 publications found

Genes affected

DAD1 (HGNC:2664): (defender against cell death 1) DAD1, the defender against apoptotic cell death, was initially identified as a negative regulator of programmed cell death in the temperature sensitive tsBN7 cell line. The DAD1 protein disappeared in temperature-sensitive cells following a shift to the nonpermissive temperature, suggesting that loss of the DAD1 protein triggered apoptosis. DAD1 is believed to be a tightly associated subunit of oligosaccharyltransferase both in the intact membrane and in the purified enzyme, thus reflecting the essential nature of N-linked glycosylation in eukaryotes. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001344.4. 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
	DAD1	NM_001344.4	MANE Select	c.212-6626G>A		intron	N/A	NP_001335.1	P61803

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAD1	ENST00000250498.9	TSL:1 MANE Select	c.212-6626G>A		intron	N/A	ENSP00000250498.4	P61803
	DAD1	ENST00000860829.1		c.212-6626G>A		intron	N/A	ENSP00000530888.1
	DAD1	ENST00000860830.1		c.212-6626G>A		intron	N/A	ENSP00000530889.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 105947 AN: 151600 Hom.: 38685 Cov.: 29

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.699 AC: 106065 AN: 151718 Hom.: 38749 Cov.: 29 AF XY: 0.697 AC XY: 51675 AN XY: 74094

African (AFR) AF: 0.929 AC: 38493 AN: 41430

American (AMR) AF: 0.609 AC: 9268 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2297 AN: 3466

East Asian (EAS) AF: 0.485 AC: 2492 AN: 5140

South Asian (SAS) AF: 0.645 AC: 3097 AN: 4804

European-Finnish (FIN) AF: 0.615 AC: 6426 AN: 10452

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41718 AN: 67888

Other (OTH) AF: 0.703 AC: 1477 AN: 2102

Alfa AF: 0.618 Hom.: 13687

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs8005354; hg19: chr14-23050763;