rs13004902

Positions:

• chr2-136270110-A-G

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 0.369 in 152,160 control chromosomes in the GnomAD database, including 14,496 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 0.37 (14496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56154 AN: 152042 Hom.: 14500 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.369 AC: 56140 AN: 152160 Hom.: 14496 Cov.: 32 AF XY: 0.361 AC XY: 26878 AN XY: 74370

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.271

Alfa AF: 0.447 Hom.: 2244

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13004902; hg19: chr2-137027680;