13-24406811-A-G

Variant names:

• chr13-24406811-A-G
• rs1816752

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 0.337 in 152,022 control chromosomes in the GnomAD database, including 8,781 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 0.34 (8781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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: 0.337 AC: 51129 AN: 151904 Hom.: 8768 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.337 AC: 51160 AN: 152022 Hom.: 8781 Cov.: 32 AF XY: 0.335 AC XY: 24923 AN XY: 74322

African (AFR) AF: 0.277 AC: 11487 AN: 41458

American (AMR) AF: 0.336 AC: 5132 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1540 AN: 5184

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4488 AN: 10538

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24842 AN: 67964

Other (OTH) AF: 0.342 AC: 722 AN: 2112

Alfa AF: 0.351 Hom.: 27986

Bravo AF: 0.325

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.31
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1816752; hg19: chr13-24980949; COSMIC: COSV71450047;