1-32993202-A-G

Variant names:

• chr1-32993202-A-G
• rs760594
• ENST00000427524.1:n.245+5883A>G

Variant summary

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

The ENST00000427524.1(ENSG00000236065):​n.245+5883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,002 control chromosomes in the GnomAD database, including 8,538 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 0.33 (8538 hom., cov: 32)
• Consequence: ENSG00000236065 ENST00000427524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

Genes affected

ENSG00000236065 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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
ENSG00000236065	ENST00000427524.1	n.245+5883A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49652 AN: 151884 Hom.: 8520 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.327 AC: 49713 AN: 152002 Hom.: 8538 Cov.: 32 AF XY: 0.330 AC XY: 24529 AN XY: 74288

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.303

Alfa AF: 0.311 Hom.: 942

Bravo AF: 0.343

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760594; hg19: chr1-33458803;