rs2157310

Positions:

• chr22-48481804-T-C

Variant summary

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

The ENST00000663363.1(ENSG00000287225):​n.262-5393A>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 0.242 in 152,206 control chromosomes in the GnomAD database, including 6,317 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 0.24 (6317 hom., cov: 33)
• Consequence: ENST00000663363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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
	ENST00000663363.1	n.262-5393A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36707 AN: 152088 Hom.: 6297 Cov.: 33

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.242 AC: 36776 AN: 152206 Hom.: 6317 Cov.: 33 AF XY: 0.239 AC XY: 17786 AN XY: 74430

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.243

Alfa AF: 0.177 Hom.: 1034

Bravo AF: 0.257

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157310; hg19: chr22-48877616;