rs1198316

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;