22-49054319-C-T

Variant names:

• chr22-49054319-C-T
• rs738617

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 0.596 in 152,122 control chromosomes in the GnomAD database, including 28,407 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 0.60 (28407 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.596 AC: 90563 AN: 152004 Hom.: 28399 Cov.: 34

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.596 AC: 90598 AN: 152122 Hom.: 28407 Cov.: 34 AF XY: 0.596 AC XY: 44355 AN XY: 74368

African (AFR) AF: 0.386 AC: 16022 AN: 41460

American (AMR) AF: 0.576 AC: 8802 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2045 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3827 AN: 5184

South Asian (SAS) AF: 0.578 AC: 2789 AN: 4822

European-Finnish (FIN) AF: 0.738 AC: 7802 AN: 10576

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47167 AN: 68000

Other (OTH) AF: 0.626 AC: 1321 AN: 2110

Alfa AF: 0.640 Hom.: 15534

Bravo AF: 0.577

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.92
DANN	Benign	0.71
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs738617; hg19: chr22-49450131;