chr8-19994534-T-A

Position:

• chr8-19994534-T-A

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 0.255 in 152,054 control chromosomes in the GnomAD database, including 4,991 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 0.25 (4991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.255 AC: 38738 AN: 151936 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.255 AC: 38749 AN: 152054 Hom.: 4991 Cov.: 32 AF XY: 0.254 AC XY: 18913 AN XY: 74342

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.251

Alfa AF: 0.258 Hom.: 609

Bravo AF: 0.252

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17489268; hg19: chr8-19852045;