rs1013696

Variant names:

• chr18-33840046-T-C
• rs1013696

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 0.256 in 151,992 control chromosomes in the GnomAD database, including 5,343 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 (5343 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.381 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: 0.256 AC: 38911 AN: 151874 Hom.: 5328 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.256 AC: 38946 AN: 151992 Hom.: 5343 Cov.: 31 AF XY: 0.258 AC XY: 19181 AN XY: 74276

African (AFR) AF: 0.227 AC: 9391 AN: 41442

American (AMR) AF: 0.390 AC: 5947 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1924 AN: 5160

South Asian (SAS) AF: 0.243 AC: 1168 AN: 4816

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10562

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16524 AN: 67966

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.251 Hom.: 10751

Bravo AF: 0.269

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1013696; hg19: chr18-31420010;