chr13-30661948-C-G

Variant names:

• chr13-30661948-C-G
• rs2985183

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 0.47 in 152,038 control chromosomes in the GnomAD database, including 20,091 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 (20091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.781 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: 0.470 AC: 71413 AN: 151920 Hom.: 20045 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.470 AC: 71509 AN: 152038 Hom.: 20091 Cov.: 32 AF XY: 0.463 AC XY: 34401 AN XY: 74302

African (AFR) AF: 0.788 AC: 32703 AN: 41482

American (AMR) AF: 0.395 AC: 6041 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1366 AN: 3472

East Asian (EAS) AF: 0.163 AC: 842 AN: 5176

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2857 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24030 AN: 67930

Other (OTH) AF: 0.459 AC: 970 AN: 2112

Alfa AF: 0.422 Hom.: 1919

Bravo AF: 0.492

Asia WGS AF: 0.364 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.52
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs2985183; hg19: chr13-31236085;