rs5756208

Positions:

• chr22-36481995-T-A
• chr22-36481995-T-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 0.76 in 151,922 control chromosomes in the GnomAD database, including 44,786 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 0.76 (44760 hom., cov: 30)
  • Exomes 𝑓: 0.74 (26 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 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: 0.760 AC: 115256 AN: 151712 Hom.: 44735 Cov.: 30

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.765

GnomAD4 exome AF: 0.739 AC: 68 AN: 92 Hom.: 26 Cov.: 0 AF XY: 0.697 AC XY: 46 AN XY: 66

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 0.553

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.913

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.760 AC: 115335 AN: 151830 Hom.: 44760 Cov.: 30 AF XY: 0.751 AC XY: 55677 AN XY: 74186

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.760

Alfa AF: 0.729 Hom.: 1690

Bravo AF: 0.765

Asia WGS AF: 0.420 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756208; hg19: chr22-36878042;