5-1295957-A-G

Position:

• chr5-1295957-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 0.884 in 152,240 control chromosomes in the GnomAD database, including 59,662 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 0.88 (59662 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134433 AN: 152122 Hom.: 59590 Cov.: 33

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.884 AC: 134566 AN: 152240 Hom.: 59662 Cov.: 33 AF XY: 0.884 AC XY: 65797 AN XY: 74440

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.852

Alfa AF: 0.856 Hom.: 14532

Bravo AF: 0.889

Asia WGS AF: 0.918 AC: 3189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7712562; hg19: chr5-1296072;