chr5-129398302-C-G

Variant names:

• chr5-129398302-C-G
• rs9632471
• ENST00000723046.1:n.137-46167G>C

Variant summary

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

The ENST00000723046.1(ADAMTS19-AS1):​n.137-46167G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,894 control chromosomes in the GnomAD database, including 11,533 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 0.37 (11533 hom., cov: 31)
• Consequence: ADAMTS19-AS1 ENST00000723046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 0 publications found

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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
ADAMTS19-AS1	ENST00000723046.1	n.137-46167G>C		intron_variant	Intron 2 of 2
ADAMTS19-AS1	ENST00000723047.1	n.1062-36728G>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55455 AN: 151776 Hom.: 11509 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.366 AC: 55527 AN: 151894 Hom.: 11533 Cov.: 31 AF XY: 0.365 AC XY: 27060 AN XY: 74216

African (AFR) AF: 0.572 AC: 23688 AN: 41384

American (AMR) AF: 0.340 AC: 5187 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3470

East Asian (EAS) AF: 0.169 AC: 871 AN: 5158

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4816

European-Finnish (FIN) AF: 0.327 AC: 3449 AN: 10548

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18745 AN: 67942

Other (OTH) AF: 0.325 AC: 688 AN: 2116

Alfa AF: 0.189 Hom.: 384

Bravo AF: 0.372

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.57
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9632471; hg19: chr5-128733995; COSMIC: COSV73837002;