19-32544943-G-C

Variant names:

• chr19-32544943-G-C
• rs1862214

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 0.332 in 151,932 control chromosomes in the GnomAD database, including 8,979 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 (8979 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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: 0.332 AC: 50363 AN: 151814 Hom.: 8955 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.332 AC: 50441 AN: 151932 Hom.: 8979 Cov.: 31 AF XY: 0.338 AC XY: 25105 AN XY: 74230

African (AFR) AF: 0.425 AC: 17598 AN: 41418

American (AMR) AF: 0.445 AC: 6803 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1914 AN: 5142

South Asian (SAS) AF: 0.340 AC: 1637 AN: 4818

European-Finnish (FIN) AF: 0.313 AC: 3308 AN: 10564

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17371 AN: 67948

Other (OTH) AF: 0.329 AC: 691 AN: 2098

Alfa AF: 0.146 Hom.: 237

Bravo AF: 0.346

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.82
DANN	Benign	0.40
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1862214; hg19: chr19-33035849;