2-81645798-C-A

Variant names:

• chr2-81645798-C-A
• rs12052359
• NR_187691.1:n.497+97051C>A

Variant summary

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

The NR_187691.1(LOC102724542):​n.497+97051C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,628 control chromosomes in the GnomAD database, including 4,862 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 0.22 (4862 hom., cov: 32)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 11 publications found

Genes affected

LOC102724542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187691.1. 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
	LOC102724542	NR_187691.1		n.497+97051C>A		intron	N/A
	LOC102724542	NR_187692.1		n.575+66189C>A		intron	N/A
	LOC102724542	NR_187693.1		n.497+97051C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34099 AN: 151512 Hom.: 4858 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.225 AC: 34107 AN: 151628 Hom.: 4862 Cov.: 32 AF XY: 0.229 AC XY: 16939 AN XY: 74064

African (AFR) AF: 0.0545 AC: 2255 AN: 41380

American (AMR) AF: 0.379 AC: 5771 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1758 AN: 5120

South Asian (SAS) AF: 0.340 AC: 1626 AN: 4786

European-Finnish (FIN) AF: 0.199 AC: 2096 AN: 10536

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18536 AN: 67812

Other (OTH) AF: 0.275 AC: 580 AN: 2106

Alfa AF: 0.262 Hom.: 17982

Bravo AF: 0.233

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs12052359; hg19: chr2-81872922;