rs1049989

Variant names:

• chr10-95237722-A-C
• rs1049989
• NM_020992.4:c.*203T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-95237722-A-C
• chr10-95237722-A-G
• chr10-95237722-A-T

Variant summary

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

The NM_020992.4(PDLIM1):​c.*203T>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 0.689 in 567,644 control chromosomes in the GnomAD database, including 144,082 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 0.64 (33639 hom., cov: 33)
  • Exomes 𝑓: 0.71 (110443 hom.)
• Consequence: PDLIM1 NM_020992.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 9 publications found

Genes affected

PDLIM1 (HGNC:2067): (PDZ and LIM domain 1) This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020992.4. 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
	PDLIM1	NM_020992.4	MANE Select	c.*203T>G		3_prime_UTR	Exon 7 of 7	NP_066272.1	O00151

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDLIM1	ENST00000329399.7	TSL:1 MANE Select	c.*203T>G		3_prime_UTR	Exon 7 of 7	ENSP00000360305.3	O00151
	PDLIM1	ENST00000956300.1		c.*203T>G		3_prime_UTR	Exon 7 of 7	ENSP00000626359.1
	PDLIM1	ENST00000862799.1		c.*203T>G		3_prime_UTR	Exon 7 of 7	ENSP00000532858.1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96886 AN: 151994 Hom.: 33621 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.680

GnomAD4 exome AF: 0.708 AC: 294059 AN: 415532 Hom.: 110443 Cov.: 4 AF XY: 0.711 AC XY: 154044 AN XY: 216710

African (AFR) AF: 0.394 AC: 4683 AN: 11876

American (AMR) AF: 0.658 AC: 11227 AN: 17070

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 9474 AN: 13042

East Asian (EAS) AF: 0.151 AC: 4463 AN: 29648

South Asian (SAS) AF: 0.701 AC: 26268 AN: 37468

European-Finnish (FIN) AF: 0.736 AC: 20577 AN: 27944

Middle Eastern (MID) AF: 0.739 AC: 1382 AN: 1870

European-Non Finnish (NFE) AF: 0.788 AC: 198760 AN: 252088

Other (OTH) AF: 0.702 AC: 17225 AN: 24526

GnomAD4 genome AF: 0.637 AC: 96945 AN: 152112 Hom.: 33639 Cov.: 33 AF XY: 0.635 AC XY: 47241 AN XY: 74356

African (AFR) AF: 0.397 AC: 16455 AN: 41468

American (AMR) AF: 0.677 AC: 10347 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.154 AC: 799 AN: 5184

South Asian (SAS) AF: 0.680 AC: 3270 AN: 4812

European-Finnish (FIN) AF: 0.724 AC: 7649 AN: 10572

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

European-Non Finnish (NFE) AF: 0.787 AC: 53515 AN: 68002

Other (OTH) AF: 0.677 AC: 1428 AN: 2110

Alfa AF: 0.713 Hom.: 19412

Bravo AF: 0.618

Asia WGS AF: 0.440 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.58
PhyloP100		0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1049989; hg19: chr10-96997479; COSMIC: COSV61475376; COSMIC: COSV61475376;