rs2099082

Variant names:

• chr5-54899963-T-C
• rs2099082
• ENST00000736670.1:n.372-32919A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-54899963-T-C
• chr5-54899963-T-G

Variant summary

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

The ENST00000736670.1(ENSG00000296132):​n.372-32919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,158 control chromosomes in the GnomAD database, including 3,907 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 0.20 (3907 hom., cov: 32)
• Consequence: ENSG00000296132 ENST00000736670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

ENSG00000296132 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736670.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296132	ENST00000736670.1		n.372-32919A>G		intron	N/A
	ENSG00000296132	ENST00000736672.1		n.228+10465A>G		intron	N/A
	ENSG00000296132	ENST00000736673.1		n.143+10465A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30587 AN: 152040 Hom.: 3904 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.201 AC: 30588 AN: 152158 Hom.: 3907 Cov.: 32 AF XY: 0.210 AC XY: 15631 AN XY: 74370

African (AFR) AF: 0.0700 AC: 2909 AN: 41542

American (AMR) AF: 0.338 AC: 5160 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.435 AC: 2250 AN: 5172

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4814

European-Finnish (FIN) AF: 0.286 AC: 3032 AN: 10584

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14375 AN: 67996

Other (OTH) AF: 0.211 AC: 444 AN: 2106

Alfa AF: 0.189 Hom.: 1579

Bravo AF: 0.199

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.26
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2099082;

hg19: chr5-54195791;