rs7523455

Variant names:

• chr1-19005582-A-G
• rs7523455
• XR_001737918.2:n.285+1676T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-19005582-A-G
• chr1-19005582-A-T

Variant summary

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

The XR_001737918.2(LOC105376815):​n.285+1676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,928 control chromosomes in the GnomAD database, including 6,366 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 0.23 (6366 hom., cov: 32)
• Consequence: LOC105376815 XR_001737918.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 8 publications found

Genes affected

LOC105376815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35339 AN: 151808 Hom.: 6359 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35380 AN: 151928 Hom.: 6366 Cov.: 32 AF XY: 0.229 AC XY: 17002 AN XY: 74262

African (AFR) AF: 0.503 AC: 20796 AN: 41340

American (AMR) AF: 0.163 AC: 2495 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1432 AN: 5174

South Asian (SAS) AF: 0.148 AC: 712 AN: 4812

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10564

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7758 AN: 67982

Other (OTH) AF: 0.209 AC: 440 AN: 2106

Alfa AF: 0.176 Hom.: 1140

Bravo AF: 0.248

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.44
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7523455; hg19: chr1-19332076; COSMIC: COSV59930046;