chr19-4883729-A-T

Variant names:

• chr19-4883729-A-T
• rs35967093

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 0.0792 in 151,918 control chromosomes in the GnomAD database, including 1,311 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 0.079 (1311 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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: 0.0792 AC: 12023 AN: 151800 Hom.: 1309 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0620

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

GnomAD4 genome AF: 0.0792 AC: 12038 AN: 151918 Hom.: 1311 Cov.: 31 AF XY: 0.0767 AC XY: 5697 AN XY: 74274

African (AFR) AF: 0.251 AC: 10371 AN: 41384

American (AMR) AF: 0.0368 AC: 562 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3466

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4812

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10592

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 804 AN: 67942

Other (OTH) AF: 0.0613 AC: 129 AN: 2104

Alfa AF: 0.0502 Hom.: 88

Bravo AF: 0.0889

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.3
DANN	Benign	0.96
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs35967093; hg19: chr19-4883741;