22-39076169-C-G

Variant names:

• chr22-39076169-C-G
• rs7291971

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 0.473 in 151,690 control chromosomes in the GnomAD database, including 20,046 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 0.47 (20046 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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: 0.473 AC: 71713 AN: 151570 Hom.: 20038 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.473 AC: 71718 AN: 151690 Hom.: 20046 Cov.: 31 AF XY: 0.475 AC XY: 35203 AN XY: 74122

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.542

Alfa AF: 0.372 Hom.: 1134

Bravo AF: 0.471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.26

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: rs7291971; hg19: chr22-39472174;