rs11176733

chr12-67420117-C-T

Variant summary

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

The XR_001749186.2(LOC105369812):n.500-1040C>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 0.111 in 152,104 control chromosomes in the GnomAD database, including 1,347 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 0.11 (1347 hom., cov: 31)
• Consequence: LOC105369812 XR_001749186.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

LOC105369812 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369812	XR_001749186.2	n.500-1040C>T		intron_variant, non_coding_transcript_variant
LOC105369812	XR_945043.3	n.500-1040C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16791 AN: 151988 Hom.: 1335 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.111 AC: 16830 AN: 152104 Hom.: 1347 Cov.: 31 AF XY: 0.108 AC XY: 8039 AN XY: 74350

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0236

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.0738

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.102 Hom.: 283

Bravo AF: 0.114

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11176733; hg19: chr12-67813897;