rs1463605

Variant names:

• chr12-29960950-C-G
• rs1463605
• XR_001749060.1:n.314-17910G>C

Variant summary

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

The XR_931474.1(LOC105369715):​n.314-17910G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,058 control chromosomes in the GnomAD database, including 2,151 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 0.16 (2151 hom., cov: 32)
• Consequence: LOC105369715 XR_931474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 10 publications found

Genes affected

LOC105369715 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24902 AN: 151940 Hom.: 2150 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.164 AC: 24922 AN: 152058 Hom.: 2151 Cov.: 32 AF XY: 0.162 AC XY: 12048 AN XY: 74336

African (AFR) AF: 0.199 AC: 8243 AN: 41428

American (AMR) AF: 0.134 AC: 2043 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.162 AC: 833 AN: 5150

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4816

European-Finnish (FIN) AF: 0.0937 AC: 994 AN: 10610

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10721 AN: 67982

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.161 Hom.: 1117

Bravo AF: 0.165

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1463605; hg19: chr12-30113883;