rs11049353

Variant names:

• chr12-28113890-A-G
• rs11049353
• XR_931461.3:n.103-6732T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-28113890-A-G
• chr12-28113890-A-T

Variant summary

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

The XR_931461.3(LOC105369710):​n.103-6732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,052 control chromosomes in the GnomAD database, including 19,620 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 0.49 (19620 hom., cov: 33)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 2 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931461.3	n.103-6732T>C		intron_variant	Intron 1 of 2
LOC105369710	XR_931462.3	n.103-6732T>C		intron_variant	Intron 1 of 2
LOC105369710	XR_931463.2	n.103-6732T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75236 AN: 151934 Hom.: 19612 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.495 AC: 75256 AN: 152052 Hom.: 19620 Cov.: 33 AF XY: 0.494 AC XY: 36718 AN XY: 74310

African (AFR) AF: 0.332 AC: 13769 AN: 41506

American (AMR) AF: 0.530 AC: 8097 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3173 AN: 5164

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5339 AN: 10526

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38506 AN: 67964

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.517 Hom.: 2607

Bravo AF: 0.488

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.12
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11049353; hg19: chr12-28266823;