rs739374

Variant names:

• chr22-19747902-G-A
• rs739374

Your query was ambiguous. Multiple possible variants found:

• chr22-19747902-G-A
• chr22-19747902-G-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 0.3 in 152,082 control chromosomes in the GnomAD database, including 7,055 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 0.30 (7055 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 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: 0.300 AC: 45557 AN: 151964 Hom.: 7040 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.300 AC: 45629 AN: 152082 Hom.: 7055 Cov.: 33 AF XY: 0.299 AC XY: 22219 AN XY: 74338

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.288

Alfa AF: 0.158 Hom.: 301

Bravo AF: 0.302

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.78
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739374; hg19: chr22-19735425;