22-43147948-G-C

Variant names:

• chr22-43147948-G-C
• rs138903

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 0.755 in 152,058 control chromosomes in the GnomAD database, including 43,679 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 0.75 (43679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.754 AC: 114625 AN: 151940 Hom.: 43621 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.755 AC: 114741 AN: 152058 Hom.: 43679 Cov.: 33 AF XY: 0.757 AC XY: 56259 AN XY: 74302

African (AFR) AF: 0.803 AC: 33290 AN: 41478

American (AMR) AF: 0.815 AC: 12428 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2480 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5123 AN: 5184

South Asian (SAS) AF: 0.848 AC: 4092 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7216 AN: 10532

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47614 AN: 67992

Other (OTH) AF: 0.772 AC: 1634 AN: 2116

Alfa AF: 0.638 Hom.: 1787

Bravo AF: 0.766

Asia WGS AF: 0.906 AC: 3149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs138903; hg19: chr22-43543954;