5-110840429-G-T

Variant names:

• chr5-110840429-G-T
• rs9885413

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 0.185 in 152,136 control chromosomes in the GnomAD database, including 4,240 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 0.18 (4240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.185 AC: 28063 AN: 152018 Hom.: 4217 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.185 AC: 28130 AN: 152136 Hom.: 4240 Cov.: 32 AF XY: 0.187 AC XY: 13878 AN XY: 74388

African (AFR) AF: 0.416 AC: 17229 AN: 41446

American (AMR) AF: 0.136 AC: 2081 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3466

East Asian (EAS) AF: 0.171 AC: 885 AN: 5176

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4824

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4974 AN: 68010

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.0976 Hom.: 2094

Bravo AF: 0.192

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.41
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs9885413; hg19: chr5-110176128;