rs6000462

Positions:

• chr22-36878305-G-A

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 0.17 in 152,116 control chromosomes in the GnomAD database, including 3,784 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 0.17 (3784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.169 AC: 25741 AN: 151998 Hom.: 3768 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.170 AC: 25798 AN: 152116 Hom.: 3784 Cov.: 32 AF XY: 0.168 AC XY: 12529 AN XY: 74376

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0989 Hom.: 1332

Bravo AF: 0.188

Asia WGS AF: 0.0970 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6000462; hg19: chr22-37274347;