rs1435033

Variant names:

• chr2-153027501-A-C
• rs1435033
• XR_007087267.1:n.194-702A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-153027501-A-C
• chr2-153027501-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_923481.1(LOC105373691):​n.310-702A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,824 control chromosomes in the GnomAD database, including 9,684 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 0.34 (9684 hom., cov: 31)
• Consequence: LOC105373691 XR_923481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02
• Publications: 4 publications found

Genes affected

LOC105373691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.341 AC: 51731 AN: 151706 Hom.: 9682 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.341 AC: 51750 AN: 151824 Hom.: 9684 Cov.: 31 AF XY: 0.335 AC XY: 24860 AN XY: 74210

African (AFR) AF: 0.194 AC: 8031 AN: 41422

American (AMR) AF: 0.340 AC: 5174 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3468

East Asian (EAS) AF: 0.186 AC: 961 AN: 5170

South Asian (SAS) AF: 0.372 AC: 1789 AN: 4814

European-Finnish (FIN) AF: 0.340 AC: 3579 AN: 10528

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29959 AN: 67884

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.352 Hom.: 6175

Bravo AF: 0.330

Asia WGS AF: 0.262 AC: 910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.5
DANN	Benign	0.95
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs1435033; hg19: chr2-153884015;