rs12632771

Variant names:

• chr3-39207361-A-G
• rs12632771
• ENST00000720013.1:n.196-2721A>G

Variant summary

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

The ENST00000720013.1(ENSG00000287620):​n.196-2721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 152,204 control chromosomes in the GnomAD database, including 701 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 0.096 (701 hom., cov: 32)
• Consequence: ENSG00000287620 ENST00000720013.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 5 publications found

Genes affected

ENSG00000287620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909366	XR_007095872.1	n.674+1878A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287620	ENST00000720013.1	n.196-2721A>G		intron_variant	Intron 2 of 2
ENSG00000293960	ENST00000720238.1	n.449-1880T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14581 AN: 152086 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0959 AC: 14589 AN: 152204 Hom.: 701 Cov.: 32 AF XY: 0.0916 AC XY: 6817 AN XY: 74424

African (AFR) AF: 0.0852 AC: 3539 AN: 41518

American (AMR) AF: 0.0807 AC: 1234 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3470

East Asian (EAS) AF: 0.0806 AC: 418 AN: 5184

South Asian (SAS) AF: 0.0510 AC: 246 AN: 4828

European-Finnish (FIN) AF: 0.0531 AC: 564 AN: 10614

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7821 AN: 67980

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.106 Hom.: 1648

Bravo AF: 0.0973

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs12632771; hg19: chr3-39248852;