rs1395538

Variant names:

• chr12-61193192-A-G
• rs1395538

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.132 in 151,922 control chromosomes in the GnomAD database, including 1,568 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 0.13 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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: 0.132 AC: 20029 AN: 151804 Hom.: 1566 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.132 AC: 20029 AN: 151922 Hom.: 1568 Cov.: 32 AF XY: 0.132 AC XY: 9833 AN XY: 74272

African (AFR) AF: 0.0527 AC: 2188 AN: 41530

American (AMR) AF: 0.122 AC: 1862 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1505 AN: 5170

South Asian (SAS) AF: 0.217 AC: 1049 AN: 4824

European-Finnish (FIN) AF: 0.145 AC: 1529 AN: 10578

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10794 AN: 67798

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.151 Hom.: 4570

Bravo AF: 0.127

Asia WGS AF: 0.189 AC: 654 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.50
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1395538; hg19: chr12-61586973;