19-21141546-A-G

Variant names:

• chr19-21141546-A-G
• rs4324267

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 0.889 in 152,028 control chromosomes in the GnomAD database, including 60,295 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 0.89 (60295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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: 0.890 AC: 135181 AN: 151914 Hom.: 60290 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.889 AC: 135226 AN: 152028 Hom.: 60295 Cov.: 31 AF XY: 0.888 AC XY: 65980 AN XY: 74328

African (AFR) AF: 0.904 AC: 37491 AN: 41454

American (AMR) AF: 0.813 AC: 12422 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4317 AN: 5180

South Asian (SAS) AF: 0.887 AC: 4273 AN: 4816

European-Finnish (FIN) AF: 0.893 AC: 9398 AN: 10520

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61085 AN: 67998

Other (OTH) AF: 0.906 AC: 1913 AN: 2112

Alfa AF: 0.895 Hom.: 87311

Bravo AF: 0.885

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.28
DANN	Benign	0.87
PhyloP100		0.32
PromoterAI		0.0012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4324267; hg19: chr19-21324349;