rs5756208

Variant names:

• chr22-36481995-T-A
• rs5756208

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;