chr19-14476390-T-A

Variant names:

• chr19-14476390-T-A
• rs10416814

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 0.334 in 145,030 control chromosomes in the GnomAD database, including 10,614 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 0.33 (10614 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.334 AC: 48394 AN: 144910 Hom.: 10569 Cov.: 23

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.334 AC: 48496 AN: 145030 Hom.: 10614 Cov.: 23 AF XY: 0.336 AC XY: 23616 AN XY: 70230

African (AFR) AF: 0.577 AC: 22132 AN: 38354

American (AMR) AF: 0.341 AC: 4869 AN: 14258

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 778 AN: 3416

East Asian (EAS) AF: 0.724 AC: 3380 AN: 4670

South Asian (SAS) AF: 0.333 AC: 1507 AN: 4520

European-Finnish (FIN) AF: 0.183 AC: 1765 AN: 9622

Middle Eastern (MID) AF: 0.187 AC: 53 AN: 284

European-Non Finnish (NFE) AF: 0.196 AC: 13119 AN: 66986

Other (OTH) AF: 0.323 AC: 653 AN: 2022

Alfa AF: 0.265 Hom.: 1002

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10416814; hg19: chr19-14587202;