rs2019091

Positions:

• chr13-22964921-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0421 in 151,170 control chromosomes in the GnomAD database, including 80 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 0.042 (80 hom., cov: 40)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0421 (6364/151170) while in subpopulation NFE AF= 0.0454 (3062/67468). AF 95% confidence interval is 0.044. There are 80 homozygotes in gnomad4. There are 3086 alleles in male gnomad4 subpopulation. Median coverage is 40. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 80 gene

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: 0.0420 AC: 6350 AN: 151050 Hom.: 79 Cov.: 40

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0681

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

GnomAD4 genome AF: 0.0421 AC: 6364 AN: 151170 Hom.: 80 Cov.: 40 AF XY: 0.0418 AC XY: 3086 AN XY: 73856

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0540 Hom.: 10

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2019091; hg19: chr13-23539060;