chr13-27784703-T-G

Variant names:

• chr13-27784703-T-G
• rs1231051

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 0.604 in 152,056 control chromosomes in the GnomAD database, including 28,115 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 0.60 (28115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91770 AN: 151938 Hom.: 28070 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.604 AC: 91880 AN: 152056 Hom.: 28115 Cov.: 32 AF XY: 0.608 AC XY: 45177 AN XY: 74334

African (AFR) AF: 0.702 AC: 29136 AN: 41486

American (AMR) AF: 0.638 AC: 9747 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3256 AN: 5182

South Asian (SAS) AF: 0.708 AC: 3408 AN: 4814

European-Finnish (FIN) AF: 0.559 AC: 5904 AN: 10564

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36884 AN: 67958

Other (OTH) AF: 0.591 AC: 1248 AN: 2110

Alfa AF: 0.560 Hom.: 73035

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1231051; hg19: chr13-28358840;