19-44843294-A-T

Variant names:

• chr19-44843294-A-T
• rs1985096

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 0.778 in 151,908 control chromosomes in the GnomAD database, including 46,898 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 0.78 (46898 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 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: 0.778 AC: 118093 AN: 151790 Hom.: 46868 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.778 AC: 118170 AN: 151908 Hom.: 46898 Cov.: 30 AF XY: 0.780 AC XY: 57936 AN XY: 74258

African (AFR) AF: 0.675 AC: 27954 AN: 41386

American (AMR) AF: 0.857 AC: 13050 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2735 AN: 3472

East Asian (EAS) AF: 0.389 AC: 1990 AN: 5120

South Asian (SAS) AF: 0.658 AC: 3173 AN: 4824

European-Finnish (FIN) AF: 0.919 AC: 9744 AN: 10602

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.836 AC: 56796 AN: 67970

Other (OTH) AF: 0.779 AC: 1640 AN: 2104

Alfa AF: 0.806 Hom.: 5860

Bravo AF: 0.770

Asia WGS AF: 0.553 AC: 1926 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	1.0
DANN	Benign	0.33
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1985096; hg19: chr19-45346551;