rs1012036

Variant names:

• chr7-52404754-C-T
• rs1012036
• XR_007060636.1:n.369-11179C>T

Variant summary

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

The XR_007060636.1(LOC124901810):​n.369-11179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,024 control chromosomes in the GnomAD database, including 3,333 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 0.19 (3333 hom., cov: 33)
• Consequence: LOC124901810 XR_007060636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 15 publications found

Genes affected

LOC124901810 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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: 0.190 AC: 28817 AN: 151908 Hom.: 3334 Cov.: 33

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.190 AC: 28823 AN: 152024 Hom.: 3333 Cov.: 33 AF XY: 0.200 AC XY: 14880 AN XY: 74306

African (AFR) AF: 0.0621 AC: 2578 AN: 41506

American (AMR) AF: 0.214 AC: 3274 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1652 AN: 5146

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4818

European-Finnish (FIN) AF: 0.350 AC: 3691 AN: 10534

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

European-Non Finnish (NFE) AF: 0.212 AC: 14395 AN: 67958

Other (OTH) AF: 0.189 AC: 399 AN: 2106

Alfa AF: 0.208 Hom.: 11672

Bravo AF: 0.168

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.71
DANN	Benign	0.78
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1012036; hg19: chr7-52472450;