8-93980339-C-G

Variant names:

• chr8-93980339-C-G
• rs4397372

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 0.596 in 151,964 control chromosomes in the GnomAD database, including 29,470 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 0.60 (29470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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: 0.596 AC: 90450 AN: 151846 Hom.: 29408 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.596 AC: 90567 AN: 151964 Hom.: 29470 Cov.: 32 AF XY: 0.597 AC XY: 44358 AN XY: 74260

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.588

Alfa AF: 0.328 Hom.: 726

Bravo AF: 0.627

Asia WGS AF: 0.758 AC: 2637 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	2.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4397372; hg19: chr8-94992567;