rs4760612

Variant names:

• chr12-48028073-C-T
• rs4760612
• XR_001749115.3:n.227-1698C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749115.3(LOC105369750):​n.227-1698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,092 control chromosomes in the GnomAD database, including 39,727 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 0.71 (39727 hom., cov: 33)
• Consequence: LOC105369750 XR_001749115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 3 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.963 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108495 AN: 151974 Hom.: 39684 Cov.: 33

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.714 AC: 108598 AN: 152092 Hom.: 39727 Cov.: 33 AF XY: 0.715 AC XY: 53179 AN XY: 74328

African (AFR) AF: 0.866 AC: 35953 AN: 41508

American (AMR) AF: 0.735 AC: 11240 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5088 AN: 5162

South Asian (SAS) AF: 0.657 AC: 3174 AN: 4828

European-Finnish (FIN) AF: 0.633 AC: 6677 AN: 10552

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42077 AN: 67966

Other (OTH) AF: 0.705 AC: 1489 AN: 2112

Alfa AF: 0.680 Hom.: 4693

Bravo AF: 0.730

Asia WGS AF: 0.790 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4760612; hg19: chr12-48421856;