chr5-16256271-A-G

Position:

• chr5-16256271-A-G

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 0.842 in 152,124 control chromosomes in the GnomAD database, including 54,653 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 0.84 (54653 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16256271A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128074 AN: 152006 Hom.: 54630 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.842 AC: 128147 AN: 152124 Hom.: 54653 Cov.: 32 AF XY: 0.842 AC XY: 62598 AN XY: 74346

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.838

Alfa AF: 0.882 Hom.: 21202

Bravo AF: 0.837

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7730897; hg19: chr5-16256380;