19-35231835-C-T

Variant names:

• chr19-35231835-C-T
• rs554313

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 0.824 in 150,122 control chromosomes in the GnomAD database, including 51,460 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 0.82 (51460 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 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: 0.824 AC: 123678 AN: 150020 Hom.: 51429 Cov.: 26

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.824 AC: 123755 AN: 150122 Hom.: 51460 Cov.: 26 AF XY: 0.827 AC XY: 60636 AN XY: 73350

African (AFR) AF: 0.705 AC: 28532 AN: 40484

American (AMR) AF: 0.907 AC: 13687 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2960 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3273 AN: 5108

South Asian (SAS) AF: 0.872 AC: 4161 AN: 4770

European-Finnish (FIN) AF: 0.866 AC: 8888 AN: 10268

Middle Eastern (MID) AF: 0.900 AC: 261 AN: 290

European-Non Finnish (NFE) AF: 0.878 AC: 59385 AN: 67658

Other (OTH) AF: 0.860 AC: 1786 AN: 2076

Alfa AF: 0.809 Hom.: 2421

Bravo AF: 0.819

Asia WGS AF: 0.778 AC: 2705 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.093
DANN	Benign	0.25
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs554313; hg19: chr19-35722738;