rs258972

chr5-6000471-A-Gchr5-6000471-A-T

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 0.965 in 152,106 control chromosomes in the GnomAD database, including 70,906 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 0.97 (70906 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146670 AN: 151988 Hom.: 70850 Cov.: 29

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.965 AC: 146786 AN: 152106 Hom.: 70906 Cov.: 29 AF XY: 0.964 AC XY: 71701 AN XY: 74358

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.990

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.965

Alfa AF: 0.978 Hom.: 12381

Bravo AF: 0.962

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258972; hg19: chr5-6000584;