XR_001741503.1:n.567-31501C>T

Variant names:

• chr4-32471518-G-A
• rs7678182
• XR_001741503.1:n.567-31501C>T

Variant summary

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

The XR_001741503.1(LOC107986223):​n.567-31501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,798 control chromosomes in the GnomAD database, including 26,537 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 0.57 (26537 hom., cov: 32)
• Consequence: LOC107986223 XR_001741503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 1 publications found

Genes affected

LOC107986223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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: 0.565 AC: 85697 AN: 151680 Hom.: 26471 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.565 AC: 85834 AN: 151798 Hom.: 26537 Cov.: 32 AF XY: 0.568 AC XY: 42133 AN XY: 74162

African (AFR) AF: 0.824 AC: 34161 AN: 41482

American (AMR) AF: 0.577 AC: 8801 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1788 AN: 3460

East Asian (EAS) AF: 0.616 AC: 3175 AN: 5154

South Asian (SAS) AF: 0.560 AC: 2697 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4706 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28896 AN: 67806

Other (OTH) AF: 0.531 AC: 1113 AN: 2098

Alfa AF: 0.439 Hom.: 7448

Bravo AF: 0.583

Asia WGS AF: 0.582 AC: 2014 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs7678182; hg19: chr4-32473140;