rs11673496

Variant names:

• chr19-22606628-G-A
• rs11673496
• ENST00000594891.1:n.208+682G>A

Variant summary

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

The ENST00000594891.1(ENSG00000269025):​n.208+682G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,348 control chromosomes in the GnomAD database, including 464 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 0.068 (464 hom., cov: 33)
• Consequence: ENSG00000269025 ENST00000594891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

Genes affected

ENSG00000269025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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
ENSG00000269025	ENST00000594891.1	n.208+682G>A		intron_variant	Intron 1 of 1	6
GOLGA2P9	ENST00000599738.1	n.334+594G>A		intron_variant	Intron 2 of 3	5
GOLGA2P9	ENST00000716029.1	n.830+682G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10299 AN: 152228 Hom.: 463 Cov.: 33

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0677 AC: 10308 AN: 152348 Hom.: 464 Cov.: 33 AF XY: 0.0670 AC XY: 4993 AN XY: 74492

African (AFR) AF: 0.0266 AC: 1107 AN: 41586

American (AMR) AF: 0.103 AC: 1573 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5180

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4828

European-Finnish (FIN) AF: 0.0607 AC: 645 AN: 10626

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5301 AN: 68030

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0762 Hom.: 271

Bravo AF: 0.0718

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs11673496; hg19: chr19-22789430;