rs35519451

Variant names:

• chr2-238205222-C-T
• rs35519451

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 0.276 in 151,958 control chromosomes in the GnomAD database, including 6,154 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 (6154 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41880 AN: 151840 Hom.: 6149 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.276 AC: 41895 AN: 151958 Hom.: 6154 Cov.: 33 AF XY: 0.276 AC XY: 20471 AN XY: 74260

African (AFR) AF: 0.177 AC: 7342 AN: 41478

American (AMR) AF: 0.252 AC: 3848 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5174

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4818

European-Finnish (FIN) AF: 0.333 AC: 3510 AN: 10532

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22589 AN: 67922

Other (OTH) AF: 0.270 AC: 570 AN: 2108

Alfa AF: 0.309 Hom.: 957

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs35519451; hg19: chr2-239113863;