rs135749

Variant names:

• chr22-38289513-G-A
• rs135749

Your query was ambiguous. Multiple possible variants found:

• chr22-38289513-G-A
• chr22-38289513-G-C

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 0.854 in 152,276 control chromosomes in the GnomAD database, including 55,728 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 0.85 (55728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.854 AC: 129874 AN: 152158 Hom.: 55664 Cov.: 33

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.854 AC: 130001 AN: 152276 Hom.: 55728 Cov.: 33 AF XY: 0.852 AC XY: 63464 AN XY: 74458

African (AFR) AF: 0.932 AC: 38725 AN: 41554

American (AMR) AF: 0.866 AC: 13237 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2640 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4590 AN: 5192

South Asian (SAS) AF: 0.733 AC: 3538 AN: 4826

European-Finnish (FIN) AF: 0.840 AC: 8905 AN: 10602

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55652 AN: 68022

Other (OTH) AF: 0.829 AC: 1755 AN: 2116

Alfa AF: 0.827 Hom.: 92206

Bravo AF: 0.865

Asia WGS AF: 0.839 AC: 2918 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	0.55
DANN	Benign	0.60
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs135749; hg19: chr22-38685519;