chr19-44728212-G-A

Variant names:

• chr19-44728212-G-A
• rs2927488

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 0.225 in 152,092 control chromosomes in the GnomAD database, including 4,036 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 0.22 (4036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34174 AN: 151974 Hom.: 4032 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.225 AC: 34184 AN: 152092 Hom.: 4036 Cov.: 32 AF XY: 0.225 AC XY: 16697 AN XY: 74346

African (AFR) AF: 0.193 AC: 8002 AN: 41450

American (AMR) AF: 0.234 AC: 3566 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3472

East Asian (EAS) AF: 0.160 AC: 830 AN: 5176

South Asian (SAS) AF: 0.281 AC: 1359 AN: 4834

European-Finnish (FIN) AF: 0.206 AC: 2180 AN: 10590

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16172 AN: 67998

Other (OTH) AF: 0.246 AC: 518 AN: 2108

Alfa AF: 0.236 Hom.: 14023

Bravo AF: 0.225

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2927488; hg19: chr19-45231478;