22-36206733-G-T

Variant names:

• chr22-36206733-G-T
• rs5995255

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 0.348 in 151,972 control chromosomes in the GnomAD database, including 9,641 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 0.35 (9641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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 = 0.42 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: 0.348 AC: 52780 AN: 151856 Hom.: 9624 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.348 AC: 52846 AN: 151972 Hom.: 9641 Cov.: 32 AF XY: 0.345 AC XY: 25618 AN XY: 74284

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.335

Alfa AF: 0.330 Hom.: 16361

Bravo AF: 0.354

Asia WGS AF: 0.135 AC: 473 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	3.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5995255; hg19: chr22-36602779;