chr5-23242296-A-G

Variant names:

• chr5-23242296-A-G
• rs7716862

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 0.853 in 152,092 control chromosomes in the GnomAD database, including 55,648 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 0.85 (55648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.906 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: 0.853 AC: 129647 AN: 151974 Hom.: 55610 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.853 AC: 129732 AN: 152092 Hom.: 55648 Cov.: 32 AF XY: 0.850 AC XY: 63230 AN XY: 74346

African (AFR) AF: 0.776 AC: 32211 AN: 41490

American (AMR) AF: 0.805 AC: 12285 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3031 AN: 3472

East Asian (EAS) AF: 0.695 AC: 3577 AN: 5144

South Asian (SAS) AF: 0.806 AC: 3882 AN: 4818

European-Finnish (FIN) AF: 0.924 AC: 9788 AN: 10592

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62043 AN: 68006

Other (OTH) AF: 0.852 AC: 1799 AN: 2112

Alfa AF: 0.876 Hom.: 14463

Bravo AF: 0.838

Asia WGS AF: 0.746 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.41
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7716862; hg19: chr5-23242405;