rs1021599

Positions:

• 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, non coding transcript 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: ENST00000646805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646805.1	n.816+73554G>A		intron_variant, non_coding_transcript_variant
	ENST00000654761.1	n.185-102258G>A		intron_variant, non_coding_transcript_variant

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;