rs1963562

Positions:

• chr12-38269094-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 0.301 in 152,074 control chromosomes in the GnomAD database, including 8,897 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 0.30 (8897 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38269094C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45766 AN: 151956 Hom.: 8895 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.301 AC: 45760 AN: 152074 Hom.: 8897 Cov.: 32 AF XY: 0.300 AC XY: 22261 AN XY: 74320

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.285

Alfa AF: 0.382 Hom.: 3218

Bravo AF: 0.279

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1963562; hg19: chr12-38662896;