rs12541063

Variant names:

• chr8-134857733-A-G
• rs12541063
• ENST00000505083.1:n.1696+6103A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-134857733-A-G
• chr8-134857733-A-T

Variant summary

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

The ENST00000505083.1(ENSG00000253433):​n.1696+6103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,144 control chromosomes in the GnomAD database, including 46,084 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 0.78 (46084 hom., cov: 31)
• Consequence: ENSG00000253433 ENST00000505083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 5 publications found

Genes affected

ENSG00000253433 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927845	NR_125427.1	n.1696+6103A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253433	ENST00000505083.1	n.1696+6103A>G		intron_variant	Intron 1 of 2	2
ENSG00000253433	ENST00000771125.1	n.376+15415A>G		intron_variant	Intron 3 of 4
ENSG00000253433	ENST00000771126.1	n.581+15415A>G		intron_variant	Intron 2 of 3
ENSG00000253433	ENST00000771240.1	n.352+6103A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118188 AN: 152026 Hom.: 46051 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118279 AN: 152144 Hom.: 46084 Cov.: 31 AF XY: 0.774 AC XY: 57533 AN XY: 74370

African (AFR) AF: 0.816 AC: 33855 AN: 41496

American (AMR) AF: 0.770 AC: 11778 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2737 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3233 AN: 5168

South Asian (SAS) AF: 0.656 AC: 3160 AN: 4816

European-Finnish (FIN) AF: 0.781 AC: 8272 AN: 10594

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.776 AC: 52777 AN: 67984

Other (OTH) AF: 0.775 AC: 1640 AN: 2116

Alfa AF: 0.769 Hom.: 14864

Bravo AF: 0.780

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs12541063; hg19: chr8-135869976;