rs56064699

Variant names:

• chr2-135838136-G-A
• rs56064699

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;