rs517871

Variant names:

• chr21-39537779-G-A
• rs517871
• ENST00000839278.1:n.629-9026C>T

Variant summary

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

The ENST00000839278.1(B3GALT5-AS1):​n.629-9026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,566 control chromosomes in the GnomAD database, including 27,561 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 0.58 (27561 hom., cov: 32)
• Consequence: B3GALT5-AS1 ENST00000839278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 3 publications found

Genes affected

B3GALT5-AS1 (HGNC:16424): (B3GALT5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.668 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
B3GALT5-AS1	ENST00000839278.1	n.629-9026C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88472 AN: 151448 Hom.: 27557 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.584 AC: 88495 AN: 151566 Hom.: 27561 Cov.: 32 AF XY: 0.592 AC XY: 43833 AN XY: 74038

African (AFR) AF: 0.353 AC: 14599 AN: 41372

American (AMR) AF: 0.678 AC: 10326 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2174 AN: 3462

East Asian (EAS) AF: 0.559 AC: 2873 AN: 5138

South Asian (SAS) AF: 0.648 AC: 3111 AN: 4804

European-Finnish (FIN) AF: 0.804 AC: 8436 AN: 10488

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 44974 AN: 67770

Other (OTH) AF: 0.600 AC: 1267 AN: 2112

Alfa AF: 0.637 Hom.: 134227

Bravo AF: 0.561

Asia WGS AF: 0.624 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.83
DANN	Benign	0.72
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs517871; hg19: chr21-40909706;