chr13-89064952-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370307	XR_001749951.2	n.148+18546G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;