rs13196564

Variant names:

• chr6-90797321-C-A
• rs13196564
• XR_001744259.1:n.1244-110735C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-90797321-C-A
• chr6-90797321-C-G
• chr6-90797321-C-T

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-110735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,088 control chromosomes in the GnomAD database, including 2,319 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 0.16 (2319 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 2 publications found

Genes affected

LOC107986623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 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: 0.163 AC: 24841 AN: 151970 Hom.: 2320 Cov.: 32

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.163 AC: 24843 AN: 152088 Hom.: 2319 Cov.: 32 AF XY: 0.172 AC XY: 12803 AN XY: 74316

African (AFR) AF: 0.0921 AC: 3823 AN: 41518

American (AMR) AF: 0.260 AC: 3975 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1640 AN: 5146

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4826

European-Finnish (FIN) AF: 0.262 AC: 2768 AN: 10568

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10469 AN: 67972

Other (OTH) AF: 0.152 AC: 320 AN: 2108

Alfa AF: 0.117 Hom.: 279

Bravo AF: 0.157

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.69
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs13196564; hg19: chr6-91507039;