rs135749

Positions:

• chr22-38289513-G-A

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 0.854 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.829

Alfa AF: 0.847 Hom.: 5038

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135749; hg19: chr22-38685519;