rs1554268

chr2-22208238-C-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):n.200+2627G>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 0.695 in 151,878 control chromosomes in the GnomAD database, including 37,944 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 0.70 (37944 hom., cov: 31)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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
	ENST00000450551.1	n.200+2627G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105462 AN: 151760 Hom.: 37879 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.695 AC: 105585 AN: 151878 Hom.: 37944 Cov.: 31 AF XY: 0.702 AC XY: 52108 AN XY: 74206

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.703

Alfa AF: 0.628 Hom.: 9521

Bravo AF: 0.709

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.86
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554268; hg19: chr2-22431110;