rs136544

Variant names:

• chr22-26855404-T-C
• rs136544

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;