rs167890

Positions:

• chr13-110796768-G-A
• chr13-110796768-G-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 0.0739 in 152,002 control chromosomes in the GnomAD database, including 451 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 0.074 (451 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11223 AN: 151884 Hom.: 448 Cov.: 30

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0739 AC: 11239 AN: 152002 Hom.: 451 Cov.: 30 AF XY: 0.0754 AC XY: 5602 AN XY: 74308

Gnomad4 AFR AF: 0.0905

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0785

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0630

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0561 Hom.: 106

Bravo AF: 0.0709

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs167890; hg19: chr13-111449115;