19-29588697-C-T

Variant names:

• chr19-29588697-C-T
• rs10403021

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 0.355 in 152,024 control chromosomes in the GnomAD database, including 9,824 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 (9824 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.354 AC: 53845 AN: 151904 Hom.: 9799 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.355 AC: 53913 AN: 152024 Hom.: 9824 Cov.: 32 AF XY: 0.349 AC XY: 25955 AN XY: 74300

African (AFR) AF: 0.427 AC: 17702 AN: 41446

American (AMR) AF: 0.267 AC: 4080 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 862 AN: 3466

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5182

South Asian (SAS) AF: 0.305 AC: 1469 AN: 4814

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10562

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

European-Non Finnish (NFE) AF: 0.357 AC: 24287 AN: 67968

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.356 Hom.: 34058

Bravo AF: 0.354

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.66
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10403021; hg19: chr19-30079604;