rs10492327

Variant names:

• chr12-114098490-C-G
• rs10492327
• ENST00000546791.1:n.63-8820C>G

Variant summary

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

The ENST00000546791.1(ENSG00000257997):​n.63-8820C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,148 control chromosomes in the GnomAD database, including 1,049 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 0.10 (1049 hom., cov: 32)
• Consequence: ENSG00000257997 ENST00000546791.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 3 publications found

Genes affected

ENSG00000257997 (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 = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369995	NR_188422.1	n.1123-8820C>G		intron_variant	Intron 2 of 4
LOC105369995	NR_188423.1	n.1123-11931C>G		intron_variant	Intron 2 of 3
LOC105369995	NR_188424.1	n.1123-8820C>G		intron_variant	Intron 2 of 3
LOC105369995	NR_188425.1	n.1123-14851C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257997	ENST00000546791.1	n.63-8820C>G		intron_variant	Intron 1 of 3	3
ENSG00000257997	ENST00000549266.6	n.502-14851C>G		intron_variant	Intron 3 of 3	3
ENSG00000257997	ENST00000552413.2	n.1107+18040C>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15531 AN: 152030 Hom.: 1052 Cov.: 32

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.102 AC: 15531 AN: 152148 Hom.: 1049 Cov.: 32 AF XY: 0.103 AC XY: 7692 AN XY: 74384

African (AFR) AF: 0.0270 AC: 1122 AN: 41532

American (AMR) AF: 0.0917 AC: 1401 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1300 AN: 5154

South Asian (SAS) AF: 0.106 AC: 512 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10572

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9138 AN: 67990

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.116 Hom.: 145

Bravo AF: 0.0965

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.58
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10492327; hg19: chr12-114536295;