rs13033116

Positions:

• chr2-238205599-T-C

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 0.277 in 150,098 control chromosomes in the GnomAD database, including 6,116 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 (6116 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41586 AN: 149994 Hom.: 6111 Cov.: 29

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 41601 AN: 150098 Hom.: 6116 Cov.: 29 AF XY: 0.277 AC XY: 20284 AN XY: 73118

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.272

Alfa AF: 0.308 Hom.: 954

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13033116; hg19: chr2-239114240;