rs578169

Positions:

• chr11-104990916-A-C
• chr11-104990916-A-G

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 0.581 in 151,972 control chromosomes in the GnomAD database, including 25,945 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 0.58 (25945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.581 AC: 88200 AN: 151856 Hom.: 25931 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.581 AC: 88250 AN: 151972 Hom.: 25945 Cov.: 32 AF XY: 0.582 AC XY: 43252 AN XY: 74286

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.608

Alfa AF: 0.568 Hom.: 3543

Bravo AF: 0.577

Asia WGS AF: 0.685 AC: 2376 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs578169; hg19: chr11-104861643;