rs1518635

Variant names:

• chr2-35657956-T-C
• rs1518635

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 0.47 in 152,054 control chromosomes in the GnomAD database, including 18,331 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 0.47 (18331 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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: 0.470 AC: 71341 AN: 151936 Hom.: 18300 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.470 AC: 71406 AN: 152054 Hom.: 18331 Cov.: 33 AF XY: 0.466 AC XY: 34616 AN XY: 74312

African (AFR) AF: 0.694 AC: 28773 AN: 41484

American (AMR) AF: 0.402 AC: 6147 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1243 AN: 3464

East Asian (EAS) AF: 0.332 AC: 1720 AN: 5180

South Asian (SAS) AF: 0.379 AC: 1824 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3651 AN: 10534

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26548 AN: 67980

Other (OTH) AF: 0.442 AC: 931 AN: 2108

Alfa AF: 0.414 Hom.: 10350

Bravo AF: 0.480

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1518635;

hg19: chr2-35883022;