rs56064699

chr2-135838136-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.15 in 151,996 control chromosomes in the GnomAD database, including 2,310 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.15 (2310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 2-135838136-G-A is Benign according to our data. Variant chr2-135838136-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 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: 0.150 AC: 22803 AN: 151878 Hom.: 2309 Cov.: 32

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.150 AC: 22804 AN: 151996 Hom.: 2310 Cov.: 32 AF XY: 0.154 AC XY: 11409 AN XY: 74274

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.226

Alfa AF: 0.145 Hom.: 321

Bravo AF: 0.149

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.5
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56064699; hg19: chr2-136595706;