chr8-27138857-T-C

Variant names:

• chr8-27138857-T-C
• rs2322509

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 0.448 in 152,148 control chromosomes in the GnomAD database, including 15,539 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 (15539 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.648 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68115 AN: 152030 Hom.: 15522 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.448 AC: 68170 AN: 152148 Hom.: 15539 Cov.: 33 AF XY: 0.450 AC XY: 33469 AN XY: 74382

African (AFR) AF: 0.431 AC: 17889 AN: 41504

American (AMR) AF: 0.538 AC: 8222 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3449 AN: 5174

South Asian (SAS) AF: 0.505 AC: 2432 AN: 4820

European-Finnish (FIN) AF: 0.349 AC: 3692 AN: 10582

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29331 AN: 67996

Other (OTH) AF: 0.467 AC: 987 AN: 2114

Alfa AF: 0.442 Hom.: 65919

Bravo AF: 0.461

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.39
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2322509; hg19: chr8-26996374;