chr19-22332449-G-T

Variant names:

• chr19-22332449-G-T
• rs1975174

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 0.597 in 151,856 control chromosomes in the GnomAD database, including 27,433 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 (27433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.74 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: 0.597 AC: 90594 AN: 151738 Hom.: 27391 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.597 AC: 90695 AN: 151856 Hom.: 27433 Cov.: 32 AF XY: 0.603 AC XY: 44709 AN XY: 74188

African (AFR) AF: 0.663 AC: 27465 AN: 41422

American (AMR) AF: 0.585 AC: 8917 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2360 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3637 AN: 5140

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5805 AN: 10510

Middle Eastern (MID) AF: 0.659 AC: 191 AN: 290

European-Non Finnish (NFE) AF: 0.544 AC: 36981 AN: 67944

Other (OTH) AF: 0.605 AC: 1273 AN: 2104

Alfa AF: 0.570 Hom.: 57666

Bravo AF: 0.595

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1975174; hg19: chr19-22515251;