rs4766921

chr12-118913063-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The XR_945423.3(LOC105370019):n.444-7135G>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 0.259 in 152,108 control chromosomes in the GnomAD database, including 5,463 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 0.26 (5463 hom., cov: 32)
• Consequence: LOC105370019 XR_945423.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15

Genes affected

LOC105370019 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370019	XR_945423.3	n.444-7135G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39397 AN: 151990 Hom.: 5465 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.259 AC: 39405 AN: 152108 Hom.: 5463 Cov.: 32 AF XY: 0.255 AC XY: 18928 AN XY: 74356

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.263

Alfa AF: 0.308 Hom.: 7463

Bravo AF: 0.259

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
Cadd	Benign	16
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4766921; hg19: chr12-119350868;