rs12632771

Positions:

• chr3-39207361-A-G

Variant summary

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

The XR_007095872.1(LOC124909366):​n.674+1878A>G 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 0.0959 in 152,204 control chromosomes in the GnomAD database, including 701 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 0.096 (701 hom., cov: 32)
• Consequence: LOC124909366 XR_007095872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

Genes affected

LOC124909366 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124909366	XR_007095872.1	n.674+1878A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14581 AN: 152086 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0959 AC: 14589 AN: 152204 Hom.: 701 Cov.: 32 AF XY: 0.0916 AC XY: 6817 AN XY: 74424

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0806

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.0531

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.101

Alfa AF: 0.108 Hom.: 1256

Bravo AF: 0.0973

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12632771; hg19: chr3-39248852;