rs3858772

Variant names:

• chr13-97674394-A-T
• rs3858772
• XR_007063845.1:n.2614+3397T>A

Variant summary

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

The XR_007063845.1(LOC105370324):​n.2614+3397T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,196 control chromosomes in the GnomAD database, including 1,260 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 0.12 (1260 hom., cov: 31)
• Consequence: LOC105370324 XR_007063845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 2 publications found

Genes affected

LOC105370324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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: 0.122 AC: 18482 AN: 152078 Hom.: 1263 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.122 AC: 18492 AN: 152196 Hom.: 1260 Cov.: 31 AF XY: 0.126 AC XY: 9354 AN XY: 74422

African (AFR) AF: 0.139 AC: 5786 AN: 41520

American (AMR) AF: 0.0923 AC: 1413 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1344 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4810

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10612

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0963 AC: 6546 AN: 68004

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.107 Hom.: 106

Bravo AF: 0.122

Asia WGS AF: 0.238 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs3858772; hg19: chr13-98326648;