rs4765158

Variant names:

• chr12-124607750-A-C
• rs4765158
• XR_242964.4:n.443-108T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-124607750-A-C
• chr12-124607750-A-T

Variant summary

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

The XR_242964.4(LOC101927436):​n.443-108T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,040 control chromosomes in the GnomAD database, including 8,662 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 0.33 (8662 hom., cov: 34)
• Consequence: LOC101927436 XR_242964.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

LOC101927436 (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 (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927436	XR_242964.4	n.443-108T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49652 AN: 151922 Hom.: 8659 Cov.: 34

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.327 AC: 49655 AN: 152040 Hom.: 8662 Cov.: 34 AF XY: 0.321 AC XY: 23851 AN XY: 74320

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.375

Alfa AF: 0.386 Hom.: 16573

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4765158; hg19: chr12-125092296;