rs1359112

Variant names:

• chr13-48715273-A-G
• rs1359112

Your query was ambiguous. Multiple possible variants found:

• chr13-48715273-A-G
• chr13-48715273-A-T

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 0.261 in 152,118 control chromosomes in the GnomAD database, including 6,518 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 0.26 (6518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• 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 = 0.507 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: 0.261 AC: 39687 AN: 152000 Hom.: 6523 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.261 AC: 39679 AN: 152118 Hom.: 6518 Cov.: 32 AF XY: 0.270 AC XY: 20054 AN XY: 74362

African (AFR) AF: 0.0670 AC: 2785 AN: 41552

American (AMR) AF: 0.316 AC: 4836 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2711 AN: 5180

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4822

European-Finnish (FIN) AF: 0.382 AC: 4034 AN: 10572

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21599 AN: 67926

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.273 Hom.: 1589

Bravo AF: 0.249

Asia WGS AF: 0.381 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1359112; hg19: chr13-49289409;