rs12760731

chr1-178502087-C-T

Variant summary

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

The XR_001738305.2(LOC101928866):n.1269-546G>A 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 0.116 in 152,244 control chromosomes in the GnomAD database, including 1,220 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 (1220 hom., cov: 33)
• Consequence: LOC101928866 XR_001738305.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

Genes affected

LOC101928866 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928866	XR_001738305.2	n.1269-546G>A		intron_variant, non_coding_transcript_variant
LOC101928866	XR_001738307.2	n.955-546G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17634 AN: 152126 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.116 AC: 17681 AN: 152244 Hom.: 1220 Cov.: 33 AF XY: 0.112 AC XY: 8344 AN XY: 74436

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.116

Alfa AF: 0.101 Hom.: 368

Bravo AF: 0.119

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12760731; hg19: chr1-178471222;