XR_002956360.2:n.183+12683C>A

Variant names:

• chr6-80593088-C-A
• rs10943724
• XR_002956360.2:n.183+12683C>A

Variant summary

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

The XR_002956360.2(LOC112267962):​n.183+12683C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,976 control chromosomes in the GnomAD database, including 6,533 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 0.26 (6533 hom., cov: 32)
• Consequence: LOC112267962 XR_002956360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 publications found

Genes affected

LOC112267962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.265 AC: 40215 AN: 151858 Hom.: 6534 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.265 AC: 40218 AN: 151976 Hom.: 6533 Cov.: 32 AF XY: 0.270 AC XY: 20045 AN XY: 74266

African (AFR) AF: 0.0894 AC: 3713 AN: 41520

American (AMR) AF: 0.393 AC: 5973 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2460 AN: 5126

South Asian (SAS) AF: 0.448 AC: 2156 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2790 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20681 AN: 67932

Other (OTH) AF: 0.322 AC: 681 AN: 2114

Alfa AF: 0.281 Hom.: 6746

Bravo AF: 0.265

Asia WGS AF: 0.421 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.41
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10943724; hg19: chr6-81302805;