rs2732167

Variant names:

• chr4-87785141-A-G
• rs2732167
• ENST00000829020.1:n.425+1168T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-87785141-A-G
• chr4-87785141-A-T

Variant summary

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

The ENST00000829020.1(ENSG00000307815):​n.425+1168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 152,200 control chromosomes in the GnomAD database, including 66,048 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 0.93 (66048 hom., cov: 31)
• Consequence: ENSG00000307815 ENST00000829020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 5 publications found

Genes affected

ENSG00000307815 (HGNC:58843):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000307815	ENST00000829020.1	n.425+1168T>C		intron_variant	Intron 4 of 5
ENSG00000307815	ENST00000829021.1	n.480+1168T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141493 AN: 152082 Hom.: 65991 Cov.: 31

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.930 AC: 141609 AN: 152200 Hom.: 66048 Cov.: 31 AF XY: 0.932 AC XY: 69338 AN XY: 74392

African (AFR) AF: 0.982 AC: 40779 AN: 41538

American (AMR) AF: 0.963 AC: 14717 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3323 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5172

South Asian (SAS) AF: 0.944 AC: 4540 AN: 4808

European-Finnish (FIN) AF: 0.880 AC: 9314 AN: 10590

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60645 AN: 68022

Other (OTH) AF: 0.930 AC: 1959 AN: 2106

Alfa AF: 0.904 Hom.: 38140

Bravo AF: 0.940

Asia WGS AF: 0.972 AC: 3381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2732167; hg19: chr4-88706293;