1-32993202-A-G

Position:

• chr1-32993202-A-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, non coding transcript 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: ENST00000427524.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000427524.1	n.245+5883A>G		intron_variant, non_coding_transcript_variant		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;