5-16256271-A-G

Variant names:

• chr5-16256271-A-G
• rs7730897

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;