chr5-16205092-A-G

Variant names:

• chr5-16205092-A-G
• rs344720

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 0.901 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.868 AC: 36027 AN: 41524

American (AMR) AF: 0.935 AC: 14306 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3087 AN: 3472

East Asian (EAS) AF: 0.949 AC: 4910 AN: 5174

South Asian (SAS) AF: 0.841 AC: 4058 AN: 4828

European-Finnish (FIN) AF: 0.896 AC: 9491 AN: 10596

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

European-Non Finnish (NFE) AF: 0.916 AC: 62345 AN: 68030

Other (OTH) AF: 0.896 AC: 1888 AN: 2108

Alfa AF: 0.913 Hom.: 105699

Bravo AF: 0.903

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs344720; hg19: chr5-16205201;