rs1891094

Variant names:

• chr1-205816804-T-C
• rs1891094
• ENST00000653632.1:n.233+3219T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-205816804-T-C
• chr1-205816804-T-G

Variant summary

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

The ENST00000653632.1(PM20D1-AS1):​n.233+3219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,102 control chromosomes in the GnomAD database, including 1,439 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 0.12 (1439 hom., cov: 31)
• Consequence: PM20D1-AS1 ENST00000653632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 7 publications found

Genes affected

PM20D1-AS1 (HGNC:27633): (PM20D1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PM20D1-AS1	ENST00000653632.1	n.233+3219T>C		intron_variant	Intron 1 of 4
PM20D1-AS1	ENST00000653838.1	n.177+3219T>C		intron_variant	Intron 1 of 4
PM20D1-AS1	ENST00000656162.1	n.238+3219T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18363 AN: 151984 Hom.: 1437 Cov.: 31

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.121 AC: 18386 AN: 152102 Hom.: 1439 Cov.: 31 AF XY: 0.124 AC XY: 9191 AN XY: 74358

African (AFR) AF: 0.0801 AC: 3322 AN: 41496

American (AMR) AF: 0.234 AC: 3579 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1566 AN: 5156

South Asian (SAS) AF: 0.189 AC: 910 AN: 4812

European-Finnish (FIN) AF: 0.0900 AC: 954 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7360 AN: 67976

Other (OTH) AF: 0.115 AC: 242 AN: 2102

Alfa AF: 0.110 Hom.: 2293

Bravo AF: 0.132

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.56
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1891094; hg19: chr1-205785932;