rs1267037

Variant names:

• chr2-161241644-A-C
• rs1267037
• ENST00000421122.8:n.385+6880T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-161241644-A-C
• chr2-161241644-A-G
• chr2-161241644-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000421122.8(PSMD14-DT):​n.385+6880T>G variant causes a intron change. The variant allele was found at a frequency of 0.701 in 152,078 control chromosomes in the GnomAD database, including 39,019 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 (39019 hom., cov: 32)
• Consequence: PSMD14-DT ENST00000421122.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.44
• Publications: 7 publications found

Genes affected

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421122.8. 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
	PSMD14-DT	NR_110593.1		n.348+6880T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD14-DT	ENST00000421122.8	TSL:3	n.385+6880T>G		intron	N/A
	PSMD14-DT	ENST00000445372.5	TSL:3	n.229+6880T>G		intron	N/A
	PSMD14-DT	ENST00000803724.1		n.271+6880T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106628 AN: 151960 Hom.: 39021 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.701 AC: 106655 AN: 152078 Hom.: 39019 Cov.: 32 AF XY: 0.703 AC XY: 52252 AN XY: 74366

African (AFR) AF: 0.471 AC: 19509 AN: 41434

American (AMR) AF: 0.795 AC: 12161 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2438 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4240 AN: 5184

South Asian (SAS) AF: 0.751 AC: 3619 AN: 4822

European-Finnish (FIN) AF: 0.724 AC: 7656 AN: 10576

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54587 AN: 67984

Other (OTH) AF: 0.708 AC: 1494 AN: 2110

Alfa AF: 0.678 Hom.: 5509

Bravo AF: 0.700

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	22
DANN	Benign	0.81
PhyloP100		5.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1267037;

hg19: chr2-162098155;