chr1-205816804-T-C

Position:

• chr1-205816804-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656763.1(PM20D1-AS1):​n.264+3219T>C variant causes a intron, non coding transcript 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 ENST00000656763.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

Genes affected

PM20D1-AS1 (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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PM20D1-AS1	ENST00000656763.1	n.264+3219T>C		intron_variant, non_coding_transcript_variant

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;