rs1395540

Positions:

• chr12-61052965-T-C

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 0.278 in 152,000 control chromosomes in the GnomAD database, including 6,358 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 0.28 (6358 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61052965T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42251 AN: 151882 Hom.: 6331 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.278 AC: 42317 AN: 152000 Hom.: 6358 Cov.: 32 AF XY: 0.278 AC XY: 20676 AN XY: 74290

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.308

Alfa AF: 0.276 Hom.: 2289

Bravo AF: 0.304

Asia WGS AF: 0.330 AC: 1149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395540; hg19: chr12-61446746;