rs2632208

Variant names:

• chr12-76607071-T-C
• rs2632208
• ENST00000551082.2:n.122-8232T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-76607071-T-C
• chr12-76607071-T-G

Variant summary

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

The ENST00000551082.2(ENSG00000257526):​n.122-8232T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,992 control chromosomes in the GnomAD database, including 3,350 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 (3350 hom., cov: 32)
• Consequence: ENSG00000257526 ENST00000551082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 3 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369850	NR_188081.1	n.453-8232T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257526	ENST00000551082.2	n.122-8232T>C		intron_variant	Intron 2 of 2	3
ENSG00000257526	ENST00000702157.2	n.496-8232T>C		intron_variant	Intron 3 of 3
ENSG00000257526	ENST00000832799.1	n.419-25850T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29889 AN: 151874 Hom.: 3335 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.197 AC: 29947 AN: 151992 Hom.: 3350 Cov.: 32 AF XY: 0.200 AC XY: 14853 AN XY: 74270

African (AFR) AF: 0.288 AC: 11929 AN: 41442

American (AMR) AF: 0.152 AC: 2326 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1837 AN: 5148

South Asian (SAS) AF: 0.260 AC: 1250 AN: 4812

European-Finnish (FIN) AF: 0.186 AC: 1960 AN: 10564

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9513 AN: 67968

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.165 Hom.: 1208

Bravo AF: 0.196

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.47
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2632208; hg19: chr12-77000851;