chr8-59217737-C-T

Position:

• chr8-59217737-C-T

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 0.423 in 151,842 control chromosomes in the GnomAD database, including 14,436 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 0.42 (14436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64138 AN: 151724 Hom.: 14401 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.423 AC: 64231 AN: 151842 Hom.: 14436 Cov.: 32 AF XY: 0.425 AC XY: 31544 AN XY: 74222

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.410

Alfa AF: 0.356 Hom.: 21506

Bravo AF: 0.443

Asia WGS AF: 0.539 AC: 1879 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3110127; hg19: chr8-60130296;