19-47601823-T-C

Variant names:

• chr19-47601823-T-C
• rs2974225

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 0.864 in 152,132 control chromosomes in the GnomAD database, including 56,982 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 0.86 (56982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 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: 0.864 AC: 131367 AN: 152014 Hom.: 56937 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.864 AC: 131472 AN: 152132 Hom.: 56982 Cov.: 32 AF XY: 0.860 AC XY: 63930 AN XY: 74362

African (AFR) AF: 0.894 AC: 37132 AN: 41516

American (AMR) AF: 0.816 AC: 12465 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3228 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3991 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3976 AN: 4810

European-Finnish (FIN) AF: 0.801 AC: 8474 AN: 10574

Middle Eastern (MID) AF: 0.897 AC: 262 AN: 292

European-Non Finnish (NFE) AF: 0.871 AC: 59242 AN: 67996

Other (OTH) AF: 0.879 AC: 1859 AN: 2114

Alfa AF: 0.873 Hom.: 156052

Bravo AF: 0.865

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.82
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs2974225; hg19: chr19-48105080;