13-27270556-A-G

Variant names:

• chr13-27270556-A-G
• rs7331765

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 0.455 in 199,084 control chromosomes in the GnomAD database, including 22,182 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 (18085 hom., cov: 33)
  • Exomes 𝑓: 0.40 (4097 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.471 AC: 71647 AN: 151988 Hom.: 18041 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.475

GnomAD4 exome AF: 0.402 AC: 18904 AN: 46976 Hom.: 4097 Cov.: 0 AF XY: 0.402 AC XY: 9539 AN XY: 23748

African (AFR) AF: 0.628 AC: 648 AN: 1032

American (AMR) AF: 0.572 AC: 388 AN: 678

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 521 AN: 1466

East Asian (EAS) AF: 0.608 AC: 825 AN: 1358

South Asian (SAS) AF: 0.393 AC: 1993 AN: 5072

European-Finnish (FIN) AF: 0.511 AC: 1632 AN: 3192

Middle Eastern (MID) AF: 0.490 AC: 102 AN: 208

European-Non Finnish (NFE) AF: 0.371 AC: 11429 AN: 30798

Other (OTH) AF: 0.431 AC: 1366 AN: 3172

GnomAD4 genome AF: 0.472 AC: 71742 AN: 152108 Hom.: 18085 Cov.: 33 AF XY: 0.477 AC XY: 35449 AN XY: 74358

African (AFR) AF: 0.638 AC: 26470 AN: 41496

American (AMR) AF: 0.534 AC: 8167 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3462

East Asian (EAS) AF: 0.603 AC: 3117 AN: 5172

South Asian (SAS) AF: 0.345 AC: 1667 AN: 4830

European-Finnish (FIN) AF: 0.479 AC: 5063 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24697 AN: 67964

Other (OTH) AF: 0.471 AC: 994 AN: 2112

Alfa AF: 0.375 Hom.: 22550

Bravo AF: 0.485

Asia WGS AF: 0.512 AC: 1783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.66
PhyloP100		-0.14
PromoterAI		-0.043	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7331765; hg19: chr13-27844693;