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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371473	XR_922214.3	n.1903+178C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;