chr5-23290034-A-G

Variant names:

• chr5-23290034-A-G
• rs10520890

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 0.179 in 152,150 control chromosomes in the GnomAD database, including 2,697 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 (2697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.179 AC: 27175 AN: 152030 Hom.: 2675 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.179 AC: 27237 AN: 152150 Hom.: 2697 Cov.: 32 AF XY: 0.182 AC XY: 13551 AN XY: 74384

African (AFR) AF: 0.231 AC: 9575 AN: 41512

American (AMR) AF: 0.190 AC: 2909 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5164

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10604

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9157 AN: 67988

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.159 Hom.: 361

Bravo AF: 0.181

Asia WGS AF: 0.314 AC: 1088 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10520890; hg19: chr5-23290143;