rs540171

Positions:

• chr9-110820111-A-C

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 0.107 in 152,264 control chromosomes in the GnomAD database, including 1,251 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 0.11 (1251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.107 AC: 16265 AN: 152146 Hom.: 1252 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0967

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.107 AC: 16279 AN: 152264 Hom.: 1251 Cov.: 33 AF XY: 0.105 AC XY: 7820 AN XY: 74452

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0696

Gnomad4 ASJ AF: 0.0967

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0427

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0799 Hom.: 753

Bravo AF: 0.112

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs540171; hg19: chr9-113582391;