rs136544

Positions:

• chr22-26855404-T-C

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 0.739 in 152,058 control chromosomes in the GnomAD database, including 41,850 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 0.74 (41850 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.739 AC: 112312 AN: 151940 Hom.: 41803 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.739 AC: 112416 AN: 152058 Hom.: 41850 Cov.: 31 AF XY: 0.739 AC XY: 54964 AN XY: 74332

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.729

Alfa AF: 0.720 Hom.: 6686

Bravo AF: 0.742

Asia WGS AF: 0.713 AC: 2475 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs136544; hg19: chr22-27251367;