XR_007066686.1:n.481+6143A>C

Variant names:

• chr1-160400029-T-G
• rs11265385
• XR_007066686.1:n.481+6143A>C

Variant summary

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

The XR_007066686.1(LOC105371466):​n.481+6143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,028 control chromosomes in the GnomAD database, including 7,879 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 0.31 (7879 hom., cov: 32)
• Consequence: LOC105371466 XR_007066686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 2 publications found

Genes affected

LOC105371466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 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: 0.313 AC: 47545 AN: 151910 Hom.: 7881 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47562 AN: 152028 Hom.: 7879 Cov.: 32 AF XY: 0.312 AC XY: 23197 AN XY: 74326

African (AFR) AF: 0.226 AC: 9375 AN: 41466

American (AMR) AF: 0.363 AC: 5545 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5158

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10584

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23973 AN: 67934

Other (OTH) AF: 0.324 AC: 683 AN: 2108

Alfa AF: 0.325 Hom.: 3134

Bravo AF: 0.316

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.2
DANN	Benign	0.80
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11265385; hg19: chr1-160369819;