rs2568112

Variant names:

• chr2-81764978-G-A
• rs2568112
• ENST00000798760.1:n.237+12150C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-81764978-G-A
• chr2-81764978-G-T

Variant summary

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

The NR_187691.1(LOC102724542):​n.498-83775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,008 control chromosomes in the GnomAD database, including 10,562 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 0.36 (10562 hom., cov: 32)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 3 publications found

Genes affected

ENSG00000303999 (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 (NFE) allele frequency at 95% confidence interval = 0.419 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724542	NR_187691.1		n.498-83775G>A		intron	N/A
	LOC102724542	NR_187692.1		n.576-83775G>A		intron	N/A
	LOC102724542	NR_187693.1		n.498-32840G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303999	ENST00000798760.1		n.237+12150C>T		intron	N/A
	ENSG00000303999	ENST00000798761.1		n.342-3136C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54930 AN: 151890 Hom.: 10559 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.361 AC: 54948 AN: 152008 Hom.: 10562 Cov.: 32 AF XY: 0.363 AC XY: 26997 AN XY: 74286

African (AFR) AF: 0.274 AC: 11354 AN: 41450

American (AMR) AF: 0.278 AC: 4238 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1135 AN: 5176

South Asian (SAS) AF: 0.321 AC: 1550 AN: 4822

European-Finnish (FIN) AF: 0.512 AC: 5399 AN: 10540

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28732 AN: 67962

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.407 Hom.: 8282

Bravo AF: 0.338

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.55
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2568112; hg19: chr2-81992102;