rs1875806

chr2-49175540-T-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):n.492+229135T>C 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 0.226 in 152,038 control chromosomes in the GnomAD database, including 4,252 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 0.23 (4252 hom., cov: 32)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.492+229135T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34286 AN: 151922 Hom.: 4252 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.226 AC: 34291 AN: 152038 Hom.: 4252 Cov.: 32 AF XY: 0.224 AC XY: 16654 AN XY: 74320

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.209

Alfa AF: 0.238 Hom.: 589

Bravo AF: 0.223

Asia WGS AF: 0.248 AC: 861 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1875806; hg19: chr2-49402679;