rs4083578

chr13-72194571-T-G

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 0.654 in 152,030 control chromosomes in the GnomAD database, including 35,332 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 0.65 (35332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99318 AN: 151912 Hom.: 35319 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.654 AC: 99358 AN: 152030 Hom.: 35332 Cov.: 32 AF XY: 0.648 AC XY: 48166 AN XY: 74292

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.677

Alfa AF: 0.782 Hom.: 67536

Bravo AF: 0.627

Asia WGS AF: 0.557 AC: 1934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	18
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4083578; hg19: chr13-72768709;