rs1395540

Variant names:

• chr12-61052965-T-C
• rs1395540

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;