rs136460

Variant names:

• chr22-32188839-T-C
• rs136460

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 0.538 in 151,992 control chromosomes in the GnomAD database, including 24,227 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 0.54 (24227 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.538 AC: 81734 AN: 151874 Hom.: 24179 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.538 AC: 81839 AN: 151992 Hom.: 24227 Cov.: 31 AF XY: 0.528 AC XY: 39222 AN XY: 74292

African (AFR) AF: 0.780 AC: 32346 AN: 41464

American (AMR) AF: 0.426 AC: 6491 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1746 AN: 3466

East Asian (EAS) AF: 0.141 AC: 728 AN: 5172

South Asian (SAS) AF: 0.382 AC: 1837 AN: 4814

European-Finnish (FIN) AF: 0.384 AC: 4051 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32988 AN: 67954

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.521 Hom.: 3859

Bravo AF: 0.550

Asia WGS AF: 0.350 AC: 1216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs136460; hg19: chr22-32584826;