rs9636436

chr2-49270867-G-A

Variant summary

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

The ENST00000634588.1(ENSG00000282890):n.493-137335G>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 0.254 in 152,100 control chromosomes in the GnomAD database, including 5,086 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 0.25 (5086 hom., cov: 33)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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.493-137335G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000635306.1	n.408-52239C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38590 AN: 151982 Hom.: 5084 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38615 AN: 152100 Hom.: 5086 Cov.: 33 AF XY: 0.255 AC XY: 18964 AN XY: 74342

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.255

Alfa AF: 0.235 Hom.: 8704

Bravo AF: 0.248

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.15
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9636436; hg19: chr2-49498006;