XR_001737985.1:n.62-24798A>T

Variant names:

• chr1-38168207-A-T
• rs12140275
• XR_001737985.1:n.62-24798A>T

Variant summary

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

The XR_001737985.1(LOC105378654):​n.62-24798A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,948 control chromosomes in the GnomAD database, including 3,654 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 0.21 (3654 hom., cov: 31)
• Consequence: LOC105378654 XR_001737985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 17 publications found

Genes affected

LOC105378654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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: 0.211 AC: 32100 AN: 151832 Hom.: 3650 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.211 AC: 32116 AN: 151948 Hom.: 3654 Cov.: 31 AF XY: 0.211 AC XY: 15678 AN XY: 74238

African (AFR) AF: 0.178 AC: 7391 AN: 41436

American (AMR) AF: 0.156 AC: 2382 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3470

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5176

South Asian (SAS) AF: 0.195 AC: 937 AN: 4806

European-Finnish (FIN) AF: 0.259 AC: 2728 AN: 10520

Middle Eastern (MID) AF: 0.210 AC: 61 AN: 290

European-Non Finnish (NFE) AF: 0.247 AC: 16763 AN: 67970

Other (OTH) AF: 0.221 AC: 466 AN: 2110

Alfa AF: 0.223 Hom.: 496

Bravo AF: 0.198

Asia WGS AF: 0.118 AC: 413 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs12140275; hg19: chr1-38633879;