chr22-36879862-C-T

Variant names:

• chr22-36879862-C-T
• rs5756379

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 0.565 in 152,052 control chromosomes in the GnomAD database, including 26,173 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 0.57 (26173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.566 AC: 85922 AN: 151934 Hom.: 26165 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.565 AC: 85943 AN: 152052 Hom.: 26173 Cov.: 32 AF XY: 0.569 AC XY: 42335 AN XY: 74354

African (AFR) AF: 0.319 AC: 13197 AN: 41432

American (AMR) AF: 0.610 AC: 9331 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2407 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3168 AN: 5166

South Asian (SAS) AF: 0.603 AC: 2904 AN: 4816

European-Finnish (FIN) AF: 0.725 AC: 7670 AN: 10586

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45365 AN: 67976

Other (OTH) AF: 0.580 AC: 1224 AN: 2110

Alfa AF: 0.636 Hom.: 132123

Bravo AF: 0.544

Asia WGS AF: 0.639 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.59
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs5756379; hg19: chr22-37275904;