13-74707684-A-G

Variant names:

• chr13-74707684-A-G
• rs2104615

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.439 in 152,114 control chromosomes in the GnomAD database, including 14,828 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 0.44 (14828 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.439 AC: 66751 AN: 151996 Hom.: 14828 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.439 AC: 66767 AN: 152114 Hom.: 14828 Cov.: 33 AF XY: 0.444 AC XY: 32974 AN XY: 74348

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.464

Alfa AF: 0.428 Hom.: 15220

Bravo AF: 0.440

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2104615; hg19: chr13-75281821;