rs1021599

Variant names:

• chr18-32635093-G-A
• rs1021599
• ENST00000646805.1:n.816+73554G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-32635093-G-A
• chr18-32635093-G-C

Variant summary

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

The ENST00000646805.1(ENSG00000285095):​n.816+73554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,816 control chromosomes in the GnomAD database, including 10,263 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 0.36 (10263 hom., cov: 31)
• Consequence: ENSG00000285095 ENST00000646805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

ENSG00000285095 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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
ENSG00000285095	ENST00000646805.1	n.816+73554G>A		intron_variant	Intron 4 of 6
ENSG00000285095	ENST00000654761.1	n.185-102258G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53942 AN: 151698 Hom.: 10230 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.356 AC: 54040 AN: 151816 Hom.: 10263 Cov.: 31 AF XY: 0.353 AC XY: 26199 AN XY: 74186

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.317

Alfa AF: 0.321 Hom.: 4686

Bravo AF: 0.362

Asia WGS AF: 0.349 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021599; hg19: chr18-30215056;