XR_922621.2:n.623-37652A>T

Variant names:

• chr1-221432490-A-T
• rs10495163
• XR_922621.2:n.623-37652A>T

Variant summary

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

The XR_922621.2(LOC105372932):​n.623-37652A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,040 control chromosomes in the GnomAD database, including 11,750 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 0.39 (11750 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

Genes affected

LOC105372932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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: 0.390 AC: 59264 AN: 151922 Hom.: 11737 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.390 AC: 59308 AN: 152040 Hom.: 11750 Cov.: 32 AF XY: 0.389 AC XY: 28875 AN XY: 74322

African (AFR) AF: 0.318 AC: 13169 AN: 41444

American (AMR) AF: 0.398 AC: 6089 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5170

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4647 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29775 AN: 67976

Other (OTH) AF: 0.396 AC: 836 AN: 2110

Alfa AF: 0.411 Hom.: 1638

Bravo AF: 0.384

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.024
DANN	Benign	0.76
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10495163; hg19: chr1-221605832; COSMIC: COSV50456249;