22-49702165-A-G

Variant names:

• chr22-49702165-A-G
• rs738415

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 0.903 in 152,222 control chromosomes in the GnomAD database, including 62,245 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 0.90 (62245 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.918 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: 0.903 AC: 137416 AN: 152104 Hom.: 62207 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.903 AC: 137511 AN: 152222 Hom.: 62245 Cov.: 33 AF XY: 0.900 AC XY: 67011 AN XY: 74418

African (AFR) AF: 0.903 AC: 37487 AN: 41532

American (AMR) AF: 0.930 AC: 14241 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3225 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3754 AN: 5154

South Asian (SAS) AF: 0.906 AC: 4374 AN: 4826

European-Finnish (FIN) AF: 0.874 AC: 9266 AN: 10606

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62168 AN: 68006

Other (OTH) AF: 0.916 AC: 1937 AN: 2114

Alfa AF: 0.915 Hom.: 40241

Bravo AF: 0.907

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs738415; hg19: chr22-50095813;