rs1012036

Positions:

• chr7-52404754-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52404754C>T		intergenic_region
LOC124901810	XR_007060636.1	n.369-11179C>T		intron_variant
LOC124901810	XR_007060637.1	n.369-11179C>T		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.189

Alfa AF: 0.215 Hom.: 8431

Bravo AF: 0.168

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012036; hg19: chr7-52472450;