2-27423903-C-T

Variant names:

• chr2-27423903-C-T
• rs6547626

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 0.471 in 151,946 control chromosomes in the GnomAD database, including 18,613 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 0.47 (18613 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71518 AN: 151828 Hom.: 18565 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.471 AC: 71632 AN: 151946 Hom.: 18613 Cov.: 31 AF XY: 0.470 AC XY: 34896 AN XY: 74282

African (AFR) AF: 0.691 AC: 28643 AN: 41446

American (AMR) AF: 0.474 AC: 7238 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.154 AC: 798 AN: 5166

South Asian (SAS) AF: 0.426 AC: 2049 AN: 4810

European-Finnish (FIN) AF: 0.430 AC: 4523 AN: 10522

Middle Eastern (MID) AF: 0.379 AC: 110 AN: 290

European-Non Finnish (NFE) AF: 0.383 AC: 26035 AN: 67964

Other (OTH) AF: 0.416 AC: 875 AN: 2104

Alfa AF: 0.441 Hom.: 2530

Bravo AF: 0.483

Asia WGS AF: 0.362 AC: 1258 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6547626; hg19: chr2-27646770;