rs2166902

Variant names:

• chr4-157785338-G-A
• rs2166902
• ENST00000652341.2:n.455+38464C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-157785338-G-A
• chr4-157785338-G-C
• chr4-157785338-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000652341.2(ENSG00000287226):​n.455+38464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 152,200 control chromosomes in the GnomAD database, including 73 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 0.026 (73 hom., cov: 32)
• Consequence: ENSG00000287226 ENST00000652341.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 1 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0263 (4008/152200) while in subpopulation NFE AF = 0.0413 (2811/68008). AF 95% confidence interval is 0.0401. There are 73 homozygotes in GnomAd4. There are 1873 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 73 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652341.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287226	ENST00000652341.2		n.455+38464C>T		intron	N/A
	ENSG00000287226	ENST00000809875.1		n.69+38464C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4010 AN: 152082 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.00806

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00788

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0263 AC: 4008 AN: 152200 Hom.: 73 Cov.: 32 AF XY: 0.0252 AC XY: 1873 AN XY: 74400

African (AFR) AF: 0.00806 AC: 335 AN: 41546

American (AMR) AF: 0.0244 AC: 373 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.00768 AC: 37 AN: 4820

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2811 AN: 68008

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.00671 Hom.: 3

Bravo AF: 0.0262

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.48
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2166902; hg19: chr4-158706490;