19-39253181-G-A

Variant names:

• chr19-39253181-G-A
• rs7248668

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 0.156 in 152,120 control chromosomes in the GnomAD database, including 2,237 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 0.16 (2237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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: 0.156 AC: 23786 AN: 152004 Hom.: 2238 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.156 AC: 23796 AN: 152120 Hom.: 2237 Cov.: 32 AF XY: 0.153 AC XY: 11375 AN XY: 74382

African (AFR) AF: 0.0685 AC: 2844 AN: 41530

American (AMR) AF: 0.258 AC: 3940 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.0658 AC: 340 AN: 5170

South Asian (SAS) AF: 0.152 AC: 731 AN: 4814

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10596

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13236 AN: 67952

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.178 Hom.: 3811

Bravo AF: 0.165

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7248668; hg19: chr19-39743821;