chr8-31418849-C-T

Variant names:

• chr8-31418849-C-T
• rs16878064

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0955 AC: 3958 AN: 41442

American (AMR) AF: 0.0326 AC: 496 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.143 AC: 736 AN: 5160

South Asian (SAS) AF: 0.0802 AC: 385 AN: 4802

European-Finnish (FIN) AF: 0.0140 AC: 148 AN: 10566

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0475 AC: 3231 AN: 67956

Other (OTH) AF: 0.0550 AC: 116 AN: 2108

Alfa AF: 0.0482 Hom.: 357

Bravo AF: 0.0638

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs16878064; hg19: chr8-31276365;