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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653632.1(ENSG00000286619):​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: ENSG00000286619 ENST00000653632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

Genes affected

ENSG00000286619 (HGNC:27633): (PM20D1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000286619	ENST00000653632.1	n.233+3219T>C		intron_variant	Intron 1 of 4
ENSG00000286619	ENST00000653838.1	n.177+3219T>C		intron_variant	Intron 1 of 4
ENSG00000286619	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

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.115

Alfa AF: 0.108 Hom.: 1619

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891094; hg19: chr1-205785932;