chr13-60209335-T-C

Variant names:

• chr13-60209335-T-C
• rs78630578

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;