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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369812	XR_001749186.2	n.500-5703A>G		intron_variant	Intron 1 of 4
LOC105369812	XR_945043.3	n.500-5703A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303038	ENST00000791334.1	n.435-5703A>G		intron_variant	Intron 1 of 2
ENSG00000303038	ENST00000791335.1	n.240-5703A>G		intron_variant	Intron 1 of 2
ENSG00000303038	ENST00000791336.1	n.298-5703A>G		intron_variant	Intron 1 of 2

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 v4.3

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;