rs10506547

Variant names:

• chr12-67415454-A-G
• rs10506547
• ENST00000791334.1:n.435-5703A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-67415454-A-G
• chr12-67415454-A-T

Variant summary

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

The ENST00000791334.1(ENSG00000303038):​n.435-5703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,132 control chromosomes in the GnomAD database, including 44,774 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 0.76 (44774 hom., cov: 32)
• Consequence: ENSG00000303038 ENST00000791334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

Genes affected

ENSG00000303038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303038	ENST00000791334.1		n.435-5703A>G		intron	N/A
	ENSG00000303038	ENST00000791335.1		n.240-5703A>G		intron	N/A
	ENSG00000303038	ENST00000791336.1		n.298-5703A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115897 AN: 152014 Hom.: 44716 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.763 AC: 116017 AN: 152132 Hom.: 44774 Cov.: 32 AF XY: 0.755 AC XY: 56125 AN XY: 74348

African (AFR) AF: 0.834 AC: 34612 AN: 41520

American (AMR) AF: 0.700 AC: 10710 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2600 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2118 AN: 5170

South Asian (SAS) AF: 0.646 AC: 3104 AN: 4806

European-Finnish (FIN) AF: 0.728 AC: 7695 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52599 AN: 67988

Other (OTH) AF: 0.756 AC: 1596 AN: 2110

Alfa AF: 0.764 Hom.: 6882

Bravo AF: 0.760

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10506547; hg19: chr12-67809234;