rs11049353

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931461.3(LOC105369710):​n.103-6732T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

Genes affected

LOC105369710 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369710	XR_931461.3	n.103-6732T>C		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931462.3	n.103-6732T>C		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931463.2	n.103-6732T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.506

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11049353; hg19: chr12-28266823;