rs12130910

Positions:

• chr1-221865030-G-A

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 0.32 in 152,026 control chromosomes in the GnomAD database, including 8,199 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 0.32 (8199 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.221865030G>A		intergenic_region
LOC124904517	XR_007066885.1	n.330+12965G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48622 AN: 151910 Hom.: 8199 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.320 AC: 48651 AN: 152026 Hom.: 8199 Cov.: 33 AF XY: 0.316 AC XY: 23488 AN XY: 74306

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.325

Alfa AF: 0.330 Hom.: 2984

Bravo AF: 0.308

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12130910; hg19: chr1-222038372; COSMIC: COSV60032690;