rs10467147

Positions:

• chr12-40373560-G-A

Variant summary

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

The XR_944868.3(LOC105369736):​n.485-18733C>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 0.295 in 151,700 control chromosomes in the GnomAD database, including 6,761 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 0.29 (6761 hom., cov: 31)
• Consequence: LOC105369736 XR_944868.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

LOC105369736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369736	XR_944868.3	n.485-18733C>T		intron_variant, non_coding_transcript_variant
LOC105369736	XR_944869.3	n.485-1508C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44710 AN: 151582 Hom.: 6758 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44732 AN: 151700 Hom.: 6761 Cov.: 31 AF XY: 0.299 AC XY: 22168 AN XY: 74128

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.284

Alfa AF: 0.308 Hom.: 9173

Bravo AF: 0.283

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	3.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10467147; hg19: chr12-40767362;