8-59255330-T-G

Variant names:

• chr8-59255330-T-G
• rs6997378

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 0.453 in 151,746 control chromosomes in the GnomAD database, including 16,024 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 0.45 (16024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 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: 0.453 AC: 68647 AN: 151626 Hom.: 16002 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.453 AC: 68721 AN: 151746 Hom.: 16024 Cov.: 32 AF XY: 0.450 AC XY: 33387 AN XY: 74168

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.503

Alfa AF: 0.451 Hom.: 1927

Bravo AF: 0.478

Asia WGS AF: 0.406 AC: 1410 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6997378; hg19: chr8-60167889;