rs2157310

Variant names:

• chr22-48481804-T-C
• rs2157310
• ENST00000659917.1:n.186-5840A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659917.1(ENSG00000287225):​n.186-5840A>G variant causes a intron 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: ENSG00000287225 ENST00000659917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 3 publications found

Genes affected

ENSG00000287225 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287225	ENST00000659917.1	n.186-5840A>G		intron_variant	Intron 1 of 1
ENSG00000287225	ENST00000662490.1	n.78-5840A>G		intron_variant	Intron 1 of 1
ENSG00000287225	ENST00000663363.1	n.262-5393A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.479 AC: 19871 AN: 41486

American (AMR) AF: 0.176 AC: 2695 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1781 AN: 5178

South Asian (SAS) AF: 0.170 AC: 823 AN: 4830

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10616

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9149 AN: 68008

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.187 Hom.: 1448

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2157310; hg19: chr22-48877616;