rs78630578

chr13-60209335-T-C

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 0.672 in 152,068 control chromosomes in the GnomAD database, including 34,631 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 0.67 (34631 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 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: 0.672 AC: 102179 AN: 151950 Hom.: 34603 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.672 AC: 102258 AN: 152068 Hom.: 34631 Cov.: 33 AF XY: 0.670 AC XY: 49787 AN XY: 74326

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.682

Alfa AF: 0.701 Hom.: 23325

Bravo AF: 0.678

Asia WGS AF: 0.589 AC: 2051 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.12
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78630578; hg19: chr13-60783469; COSMIC: COSV69355525;