19-45655255-T-G

Variant names:

• chr19-45655255-T-G
• rs8108269

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 0.349 in 151,958 control chromosomes in the GnomAD database, including 9,489 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 (9489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 78 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.349 AC: 53004 AN: 151840 Hom.: 9481 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.349 AC: 53035 AN: 151958 Hom.: 9489 Cov.: 32 AF XY: 0.350 AC XY: 25960 AN XY: 74248

African (AFR) AF: 0.422 AC: 17452 AN: 41400

American (AMR) AF: 0.365 AC: 5563 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2449 AN: 5162

South Asian (SAS) AF: 0.335 AC: 1616 AN: 4826

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10566

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20343 AN: 67960

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.320 Hom.: 31340

Bravo AF: 0.358

Asia WGS AF: 0.396 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs8108269; hg19: chr19-46158513;