12-92496744-T-C

Variant names:

• chr12-92496744-T-C
• rs10219495
• ENST00000758465.1:n.142+6357A>G

Variant summary

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

The ENST00000758465.1(ENSG00000310529):​n.142+6357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,278 control chromosomes in the GnomAD database, including 63,704 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 0.91 (63704 hom., cov: 32)
• Consequence: ENSG00000310529 ENST00000758465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 7 publications found

Genes affected

ENSG00000310529 (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 (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310529	ENST00000758465.1	n.142+6357A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139058 AN: 152160 Hom.: 63638 Cov.: 32

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.914 AC: 139186 AN: 152278 Hom.: 63704 Cov.: 32 AF XY: 0.914 AC XY: 68046 AN XY: 74450

African (AFR) AF: 0.967 AC: 40185 AN: 41566

American (AMR) AF: 0.923 AC: 14110 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3005 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5153 AN: 5188

South Asian (SAS) AF: 0.886 AC: 4277 AN: 4826

European-Finnish (FIN) AF: 0.895 AC: 9482 AN: 10596

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59984 AN: 68022

Other (OTH) AF: 0.906 AC: 1914 AN: 2112

Alfa AF: 0.895 Hom.: 191387

Bravo AF: 0.920

Asia WGS AF: 0.934 AC: 3246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.65
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10219495; hg19: chr12-92890520;