rs10077875

Variant names:

• chr5-129387003-G-A
• rs10077875
• ENST00000722821.1:n.653-5648G>A

Variant summary

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

The ENST00000722821.1(ENSG00000286274):​n.653-5648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,984 control chromosomes in the GnomAD database, including 18,035 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 0.49 (18035 hom., cov: 32)
• Consequence: ENSG00000286274 ENST00000722821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 10 publications found

Genes affected

ENSG00000286274 (HGNC:):

ADAMTS19-AS1 (HGNC:40797): (ADAMTS19 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286274	ENST00000722821.1		n.653-5648G>A		intron	N/A
	ENSG00000286274	ENST00000722822.1		n.272-1445G>A		intron	N/A
	ADAMTS19-AS1	ENST00000723046.1		n.137-34868C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73725 AN: 151866 Hom.: 18013 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.486 AC: 73793 AN: 151984 Hom.: 18035 Cov.: 32 AF XY: 0.486 AC XY: 36112 AN XY: 74294

African (AFR) AF: 0.535 AC: 22169 AN: 41454

American (AMR) AF: 0.494 AC: 7543 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2971 AN: 5164

South Asian (SAS) AF: 0.443 AC: 2135 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4929 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30861 AN: 67942

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.468 Hom.: 71191

Bravo AF: 0.493

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10077875; hg19: chr5-128722696;