13-27805572-A-G

Variant names:

• chr13-27805572-A-G
• rs1231064

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 0.289 in 152,082 control chromosomes in the GnomAD database, including 6,470 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 0.29 (6470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.289 AC: 43986 AN: 151964 Hom.: 6465 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.289 AC: 44012 AN: 152082 Hom.: 6470 Cov.: 32 AF XY: 0.292 AC XY: 21726 AN XY: 74360

African (AFR) AF: 0.258 AC: 10715 AN: 41504

American (AMR) AF: 0.280 AC: 4281 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 946 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2234 AN: 5168

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4818

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19907 AN: 67958

Other (OTH) AF: 0.262 AC: 551 AN: 2106

Alfa AF: 0.279 Hom.: 6623

Bravo AF: 0.286

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.3
DANN	Benign	0.89
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1231064; hg19: chr13-28379709;