10-89197646-G-T

Variant names:

• chr10-89197646-G-T
• rs7091822
• XR_946180.4:n.355+2938G>T

Variant summary

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

The XR_946180.4(LOC105378418):​n.355+2938G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,064 control chromosomes in the GnomAD database, including 7,462 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 0.27 (7462 hom., cov: 30)
• Consequence: LOC105378418 XR_946180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 6 publications found

Genes affected

LOC105378418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.274 AC: 41292 AN: 150966 Hom.: 7433 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.274 AC: 41373 AN: 151064 Hom.: 7462 Cov.: 30 AF XY: 0.282 AC XY: 20806 AN XY: 73710

African (AFR) AF: 0.418 AC: 17188 AN: 41104

American (AMR) AF: 0.294 AC: 4465 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3466

East Asian (EAS) AF: 0.790 AC: 4056 AN: 5134

South Asian (SAS) AF: 0.354 AC: 1698 AN: 4792

European-Finnish (FIN) AF: 0.281 AC: 2868 AN: 10210

Middle Eastern (MID) AF: 0.247 AC: 71 AN: 288

European-Non Finnish (NFE) AF: 0.141 AC: 9599 AN: 67854

Other (OTH) AF: 0.256 AC: 538 AN: 2100

Alfa AF: 0.186 Hom.: 11479

Bravo AF: 0.285

Asia WGS AF: 0.507 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.35
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7091822; hg19: chr10-90957403;