rs356570

chr5-64151962-A-Gchr5-64151962-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 0.451 in 151,976 control chromosomes in the GnomAD database, including 16,945 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 0.45 (16945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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: 0.451 AC: 68513 AN: 151856 Hom.: 16906 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.451 AC: 68605 AN: 151976 Hom.: 16945 Cov.: 32 AF XY: 0.442 AC XY: 32815 AN XY: 74268

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.442

Alfa AF: 0.423 Hom.: 2360

Bravo AF: 0.472

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.36
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs356570; hg19: chr5-63447789;