8-31418849-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 0.0607 in 151,948 control chromosomes in the GnomAD database, including 362 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 0.061 (362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0606 AC: 9207 AN: 151830 Hom.: 360 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0607 AC: 9216 AN: 151948 Hom.: 362 Cov.: 32 AF XY: 0.0593 AC XY: 4404 AN XY: 74250

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0802

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0465 Hom.: 263

Bravo AF: 0.0638

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.072
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16878064; hg19: chr8-31276365;