19-34890948-T-C

Variant names:

• chr19-34890948-T-C
• rs888861

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 0.433 in 152,022 control chromosomes in the GnomAD database, including 15,773 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 0.43 (15773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.433 AC: 65714 AN: 151904 Hom.: 15748 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.433 AC: 65779 AN: 152022 Hom.: 15773 Cov.: 32 AF XY: 0.431 AC XY: 32016 AN XY: 74326

African (AFR) AF: 0.659 AC: 27328 AN: 41454

American (AMR) AF: 0.315 AC: 4816 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1275 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1863 AN: 5142

South Asian (SAS) AF: 0.448 AC: 2160 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3979 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23151 AN: 67954

Other (OTH) AF: 0.403 AC: 851 AN: 2112

Alfa AF: 0.400 Hom.: 2308

Bravo AF: 0.495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.63
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs888861; hg19: chr19-35381852;