rs2117047

Positions:

• chr12-76003767-G-A
• chr12-76003767-G-T

Variant summary

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

The XR_945110.4(LOC105369847):​n.403-345C>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 0.502 in 151,874 control chromosomes in the GnomAD database, including 19,281 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 0.50 (19281 hom., cov: 31)
• Consequence: LOC105369847 XR_945110.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

LOC105369847 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369847	XR_945110.4	n.403-345C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76161 AN: 151754 Hom.: 19283 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.502 AC: 76170 AN: 151874 Hom.: 19281 Cov.: 31 AF XY: 0.503 AC XY: 37316 AN XY: 74196

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.545

Alfa AF: 0.505 Hom.: 13950

Bravo AF: 0.495

Asia WGS AF: 0.561 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
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: rs2117047; hg19: chr12-76397547;