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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.906

Alfa AF: 0.899 Hom.: 27556

Bravo AF: 0.913

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1198316; hg19: chr13-50370205;