rs540171

Variant names:

• chr9-110820111-A-C
• rs540171

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.206 AC: 8535 AN: 41526

American (AMR) AF: 0.0696 AC: 1064 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0967 AC: 335 AN: 3464

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5186

South Asian (SAS) AF: 0.114 AC: 552 AN: 4828

European-Finnish (FIN) AF: 0.0427 AC: 453 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4759 AN: 68028

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.0828 Hom.: 1013

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
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs540171; hg19: chr9-113582391;