chr5-19384634-G-A

Variant names:

• chr5-19384634-G-A
• rs2221880

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 0.328 in 151,900 control chromosomes in the GnomAD database, including 8,747 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 0.33 (8747 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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: 0.328 AC: 49860 AN: 151782 Hom.: 8749 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.328 AC: 49881 AN: 151900 Hom.: 8747 Cov.: 31 AF XY: 0.328 AC XY: 24349 AN XY: 74232

African (AFR) AF: 0.238 AC: 9869 AN: 41410

American (AMR) AF: 0.433 AC: 6613 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3464

East Asian (EAS) AF: 0.0944 AC: 487 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3751 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25523 AN: 67934

Other (OTH) AF: 0.310 AC: 654 AN: 2108

Alfa AF: 0.359 Hom.: 1226

Bravo AF: 0.329

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.31
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2221880; hg19: chr5-19384743;