XR_001738106.2:n.1308-212C>T

Variant names:

• chr1-69549303-C-T
• rs947420
• XR_001738106.2:n.1308-212C>T

Variant summary

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

The XR_001738106.2(LOC105378789):​n.1308-212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,914 control chromosomes in the GnomAD database, including 7,356 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 0.30 (7356 hom., cov: 32)
• Consequence: LOC105378789 XR_001738106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 6 publications found

Genes affected

LOC105378789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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: 0.304 AC: 46204 AN: 151798 Hom.: 7344 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.304 AC: 46252 AN: 151914 Hom.: 7356 Cov.: 32 AF XY: 0.302 AC XY: 22386 AN XY: 74240

African (AFR) AF: 0.223 AC: 9247 AN: 41454

American (AMR) AF: 0.304 AC: 4623 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3466

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5162

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4826

European-Finnish (FIN) AF: 0.291 AC: 3074 AN: 10570

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

European-Non Finnish (NFE) AF: 0.347 AC: 23559 AN: 67906

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.315 Hom.: 1267

Bravo AF: 0.303

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.44
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs947420; hg19: chr1-70014986; COSMIC: COSV59953744;