1-160399582-T-G

Variant names:

• chr1-160399582-T-G
• rs11582932
• XR_007066686.1:n.481+6590A>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+6590A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,084 control chromosomes in the GnomAD database, including 9,122 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 0.34 (9122 hom., cov: 32)
• Consequence: LOC105371466 XR_007066686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 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: 0.342 AC: 51979 AN: 151966 Hom.: 9124 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152084 Hom.: 9122 Cov.: 32 AF XY: 0.341 AC XY: 25369 AN XY: 74324

African (AFR) AF: 0.321 AC: 13301 AN: 41462

American (AMR) AF: 0.379 AC: 5786 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1446 AN: 5194

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4818

European-Finnish (FIN) AF: 0.277 AC: 2931 AN: 10576

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24012 AN: 67978

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.355 Hom.: 16470

Bravo AF: 0.349

Asia WGS AF: 0.375 AC: 1304 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	5.9
DANN	Benign	0.55
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs11582932; hg19: chr1-160369372;