rs11047543

chr12-24635405-G-A

Variant summary

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

The XR_001749046.2(LOC105369698):n.327-17595C>T 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 0.12 in 151,788 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 32)
• Consequence: LOC105369698 XR_001749046.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

LOC105369698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369698	XR_001749046.2	n.327-17595C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18172 AN: 151670 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.120 AC: 18181 AN: 151788 Hom.: 1307 Cov.: 32 AF XY: 0.120 AC XY: 8936 AN XY: 74200

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.148

Alfa AF: 0.146 Hom.: 1996

Bravo AF: 0.120

Asia WGS AF: 0.191 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11047543; hg19: chr12-24788339;