rs7535475

Variant names:

• chr1-161493797-C-A
• rs7535475
• XR_922214.3:n.1903+178C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-161493797-C-A
• chr1-161493797-C-T

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+178C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,026 control chromosomes in the GnomAD database, including 20,216 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 0.51 (20216 hom., cov: 33)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 9 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.506 AC: 76877 AN: 151908 Hom.: 20215 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.506 AC: 76918 AN: 152026 Hom.: 20216 Cov.: 33 AF XY: 0.501 AC XY: 37206 AN XY: 74336

African (AFR) AF: 0.393 AC: 16290 AN: 41474

American (AMR) AF: 0.573 AC: 8755 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5178

South Asian (SAS) AF: 0.416 AC: 2007 AN: 4828

European-Finnish (FIN) AF: 0.517 AC: 5459 AN: 10556

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39613 AN: 67930

Other (OTH) AF: 0.524 AC: 1108 AN: 2114

Alfa AF: 0.449 Hom.: 2067

Bravo AF: 0.507

Asia WGS AF: 0.352 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs7535475; hg19: chr1-161463587;