rs796185

Variant names:

• chr13-89064952-G-A
• rs796185
• XR_001749951.2:n.148+18546G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-89064952-G-A
• chr13-89064952-G-C

Variant summary

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

The XR_001749951.2(LOC105370307):​n.148+18546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 152,082 control chromosomes in the GnomAD database, including 68,167 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 0.95 (68167 hom., cov: 33)
• Consequence: LOC105370307 XR_001749951.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 0 publications found

Genes affected

LOC105370307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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: 0.945 AC: 143623 AN: 151964 Hom.: 68126 Cov.: 33

Gnomad AFR AF: 0.901

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.945 AC: 143720 AN: 152082 Hom.: 68167 Cov.: 33 AF XY: 0.941 AC XY: 69935 AN XY: 74340

African (AFR) AF: 0.901 AC: 37420 AN: 41532

American (AMR) AF: 0.971 AC: 14793 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3123 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3861 AN: 5178

South Asian (SAS) AF: 0.894 AC: 4317 AN: 4828

European-Finnish (FIN) AF: 0.949 AC: 10073 AN: 10610

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 66957 AN: 67910

Other (OTH) AF: 0.941 AC: 1986 AN: 2110

Alfa AF: 0.965 Hom.: 14143

Bravo AF: 0.946

Asia WGS AF: 0.855 AC: 2961 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.1
DANN	Benign	0.81
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs796185; hg19: chr13-89717206;