rs1054442

Variant names:

• chr12-48995537-A-C
• rs1054442
• NM_015086.2:c.*1203T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-48995537-A-C
• chr12-48995537-A-G
• chr12-48995537-A-T

Variant summary

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

The NM_015086.2(DDN):​c.*1203T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,290 control chromosomes in the GnomAD database, including 16,555 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 0.45 (16540 hom., cov: 33)
  • Exomes 𝑓: 0.43 (15 hom.)
• Consequence: DDN NM_015086.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 28 publications found

Genes affected

DDN (HGNC:24458): (dendrin) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in cell projection and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000258283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DDN	NM_015086.2	c.*1203T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000421952.3	NP_055901.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDN	ENST00000421952.3	c.*1203T>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_015086.2	ENSP00000390590.2
ENSG00000258283	ENST00000549516.1	n.205+183A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68689 AN: 152022 Hom.: 16504 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.389

GnomAD4 exome AF: 0.433 AC: 65 AN: 150 Hom.: 15 Cov.: 0 AF XY: 0.445 AC XY: 49 AN XY: 110

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.405 AC: 51 AN: 126

Other (OTH) AF: 0.417 AC: 5 AN: 12

GnomAD4 genome AF: 0.452 AC: 68780 AN: 152140 Hom.: 16540 Cov.: 33 AF XY: 0.452 AC XY: 33596 AN XY: 74376

African (AFR) AF: 0.622 AC: 25835 AN: 41504

American (AMR) AF: 0.354 AC: 5422 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2192 AN: 5166

South Asian (SAS) AF: 0.506 AC: 2442 AN: 4824

European-Finnish (FIN) AF: 0.433 AC: 4591 AN: 10594

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25896 AN: 67966

Other (OTH) AF: 0.388 AC: 817 AN: 2108

Alfa AF: 0.388 Hom.: 19007

Bravo AF: 0.444

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.2
DANN	Benign	0.35
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1054442; hg19: chr12-49389320;