22-16912130-G-T

Variant names:

• chr22-16912130-G-T
• rs5748736

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.472 in 149,192 control chromosomes in the GnomAD database, including 17,062 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 (17062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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: 0.472 AC: 70323 AN: 149078 Hom.: 17058 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.472 AC: 70346 AN: 149192 Hom.: 17062 Cov.: 32 AF XY: 0.479 AC XY: 34907 AN XY: 72880

African (AFR) AF: 0.311 AC: 12408 AN: 39916

American (AMR) AF: 0.548 AC: 8259 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2049 AN: 3450

East Asian (EAS) AF: 0.648 AC: 3298 AN: 5092

South Asian (SAS) AF: 0.600 AC: 2859 AN: 4762

European-Finnish (FIN) AF: 0.493 AC: 5096 AN: 10340

Middle Eastern (MID) AF: 0.534 AC: 155 AN: 290

European-Non Finnish (NFE) AF: 0.515 AC: 34635 AN: 67312

Other (OTH) AF: 0.491 AC: 1012 AN: 2062

Alfa AF: 0.482 Hom.: 6779

Bravo AF: 0.464

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.83
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs5748736; hg19: chr22-17393020;