rs10492327

chr12-114098490-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549266.5(ENSG00000257997):n.71-14851C>G variant causes a intron, non coding transcript 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: ENST00000549266.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369995	XR_945361.3	n.1096-14851C>G		intron_variant, non_coding_transcript_variant
LOC105369995	XR_945360.4	n.1096-8820C>G		intron_variant, non_coding_transcript_variant
LOC105369995	XR_945363.4	n.1096-11931C>G		intron_variant, non_coding_transcript_variant
LOC105369995	XR_945365.4	n.1096-8820C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549266.5	n.71-14851C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000546791.1	n.63-8820C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0270

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.0964

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492327; hg19: chr12-114536295;