rs56064699

Variant names:

• chr2-135838136-G-A
• rs56064699

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 0.15 in 151,996 control chromosomes in the GnomAD database, including 2,310 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 0.15 (2310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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

African (AFR) AF: 0.0541 AC: 2243 AN: 41422

American (AMR) AF: 0.223 AC: 3403 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5162

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1420 AN: 10546

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11176 AN: 67988

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.140 Hom.: 1142

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs56064699; hg19: chr2-136595706;