XR_001744232.2:n.232-454T>G

Variant names:

• chr6-82686423-A-C
• rs771443
• XR_001744232.2:n.232-454T>G

Variant summary

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

The XR_001744232.2(LOC105377876):​n.232-454T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,994 control chromosomes in the GnomAD database, including 28,607 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 0.60 (28607 hom., cov: 32)
• Consequence: LOC105377876 XR_001744232.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 3 publications found

Genes affected

LOC105377876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.597 AC: 90619 AN: 151876 Hom.: 28602 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.597 AC: 90665 AN: 151994 Hom.: 28607 Cov.: 32 AF XY: 0.598 AC XY: 44418 AN XY: 74284

African (AFR) AF: 0.373 AC: 15457 AN: 41468

American (AMR) AF: 0.680 AC: 10394 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3468

East Asian (EAS) AF: 0.830 AC: 4277 AN: 5156

South Asian (SAS) AF: 0.735 AC: 3541 AN: 4820

European-Finnish (FIN) AF: 0.614 AC: 6478 AN: 10548

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45989 AN: 67922

Other (OTH) AF: 0.626 AC: 1323 AN: 2114

Alfa AF: 0.575 Hom.: 3345

Bravo AF: 0.590

Asia WGS AF: 0.760 AC: 2643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs771443; hg19: chr6-83396140;