5-16205092-A-G

Variant names:

• chr5-16205092-A-G
• rs344720

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.901 in 152,232 control chromosomes in the GnomAD database, including 61,892 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 0.90 (61892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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: 0.901 AC: 137097 AN: 152114 Hom.: 61850 Cov.: 33

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.901 AC: 137191 AN: 152232 Hom.: 61892 Cov.: 33 AF XY: 0.900 AC XY: 66960 AN XY: 74420

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.896

Alfa AF: 0.914 Hom.: 83026

Bravo AF: 0.903

Asia WGS AF: 0.864 AC: 3005 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	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344720; hg19: chr5-16205201;