5-110810746-C-G

Variant names:

• chr5-110810746-C-G
• rs17513503

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 0.092 in 152,096 control chromosomes in the GnomAD database, including 729 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 0.092 (729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.0919 AC: 13970 AN: 151978 Hom.: 727 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.0920 AC: 13986 AN: 152096 Hom.: 729 Cov.: 32 AF XY: 0.0920 AC XY: 6840 AN XY: 74356

African (AFR) AF: 0.130 AC: 5402 AN: 41502

American (AMR) AF: 0.0774 AC: 1181 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 570 AN: 3464

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0294 AC: 142 AN: 4828

European-Finnish (FIN) AF: 0.0804 AC: 851 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0823 AC: 5595 AN: 67972

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0699 Hom.: 252

Bravo AF: 0.0930

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs17513503; hg19: chr5-110146446;