rs1198316

Variant names:

• chr13-49796069-A-G
• rs1198316

Your query was ambiguous. Multiple possible variants found:

• chr13-49796069-A-G
• chr13-49796069-A-T

Variant summary

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

The variant allele was found at a frequency of 0.91 in 152,166 control chromosomes in the GnomAD database, including 63,013 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 0.91 (63013 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.932 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: 0.910 AC: 138294 AN: 152048 Hom.: 62960 Cov.: 30

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.910 AC: 138406 AN: 152166 Hom.: 63013 Cov.: 30 AF XY: 0.912 AC XY: 67813 AN XY: 74384

African (AFR) AF: 0.917 AC: 38072 AN: 41534

American (AMR) AF: 0.945 AC: 14444 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3350 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4830 AN: 5164

South Asian (SAS) AF: 0.874 AC: 4205 AN: 4810

European-Finnish (FIN) AF: 0.921 AC: 9769 AN: 10602

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60924 AN: 67988

Other (OTH) AF: 0.906 AC: 1909 AN: 2108

Alfa AF: 0.899 Hom.: 31023

Bravo AF: 0.913

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1198316; hg19: chr13-50370205;