rs1372339

Variant names:

• chr8-19974287-A-G
• rs1372339

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.164 in 152,060 control chromosomes in the GnomAD database, including 2,102 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 (2102 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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: 0.164 AC: 24934 AN: 151942 Hom.: 2099 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.164 AC: 24958 AN: 152060 Hom.: 2102 Cov.: 31 AF XY: 0.163 AC XY: 12125 AN XY: 74348

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0986

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.163

Alfa AF: 0.169 Hom.: 330

Bravo AF: 0.164

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372339; hg19: chr8-19831798;