rs11620883

Positions:

• chr14-69255063-C-T

Variant summary

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

The ENST00000556316.1(ENSG00000258520):​n.526+1991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,280 control chromosomes in the GnomAD database, including 336 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 0.064 (336 hom., cov: 32)
• Consequence: ENSG00000258520 ENST00000556316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.872

Genes affected

ENSG00000258520 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT16-AS1	NR_184249.1	n.486+1991G>A		intron_variant
GALNT16-AS1	NR_184250.1	n.992+1991G>A		intron_variant
GALNT16-AS1	NR_184251.1	n.992+1991G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258520	ENST00000556316.1	n.526+1991G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9741 AN: 152162 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0884

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0640 AC: 9745 AN: 152280 Hom.: 336 Cov.: 32 AF XY: 0.0627 AC XY: 4666 AN XY: 74464

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.00953

Gnomad4 FIN AF: 0.0884

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0596 Hom.: 403

Bravo AF: 0.0590

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
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: rs11620883; hg19: chr14-69721780;