XR_001737985.1:n.62-19469G>A

Variant names:

• chr1-38173536-G-A
• rs7544568
• XR_001737985.1:n.62-19469G>A

Variant summary

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

The XR_001737985.1(LOC105378654):​n.62-19469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,118 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 32)
• Consequence: LOC105378654 XR_001737985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 7 publications found

Genes affected

LOC105378654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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: 0.198 AC: 30078 AN: 152000 Hom.: 3334 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.198 AC: 30094 AN: 152118 Hom.: 3337 Cov.: 32 AF XY: 0.197 AC XY: 14678 AN XY: 74340

African (AFR) AF: 0.127 AC: 5256 AN: 41516

American (AMR) AF: 0.153 AC: 2332 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.0123 AC: 64 AN: 5184

South Asian (SAS) AF: 0.196 AC: 943 AN: 4818

European-Finnish (FIN) AF: 0.259 AC: 2735 AN: 10560

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16919 AN: 67982

Other (OTH) AF: 0.218 AC: 461 AN: 2116

Alfa AF: 0.222 Hom.: 4934

Bravo AF: 0.183

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.96
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7544568; hg19: chr1-38639208;