19-2996891-C-T

Variant names:

• chr19-2996891-C-T
• rs4806893

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 0.625 in 152,094 control chromosomes in the GnomAD database, including 30,642 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 0.63 (30642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.37
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.625 AC: 94989 AN: 151976 Hom.: 30605 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.625 AC: 95085 AN: 152094 Hom.: 30642 Cov.: 32 AF XY: 0.621 AC XY: 46167 AN XY: 74328

African (AFR) AF: 0.781 AC: 32416 AN: 41528

American (AMR) AF: 0.602 AC: 9186 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1956 AN: 3464

East Asian (EAS) AF: 0.698 AC: 3602 AN: 5162

South Asian (SAS) AF: 0.458 AC: 2209 AN: 4826

European-Finnish (FIN) AF: 0.533 AC: 5634 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38063 AN: 67954

Other (OTH) AF: 0.618 AC: 1302 AN: 2108

Alfa AF: 0.619 Hom.: 5264

Bravo AF: 0.642

Asia WGS AF: 0.608 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.080
DANN	Benign	0.49
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs4806893; hg19: chr19-2996889;