1-78888403-C-T

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 0.0399 in 152,100 control chromosomes in the GnomAD database, including 154 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 0.040 (154 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0521 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: 0.0399 AC: 6058 AN: 151984 Hom.: 154 Cov.: 33

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0399 AC: 6064 AN: 152100 Hom.: 154 Cov.: 33 AF XY: 0.0390 AC XY: 2898 AN XY: 74342

Gnomad4 AFR AF: 0.0187

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0536

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.00969 Hom.: 2

Bravo AF: 0.0402

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.27
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518590; hg19: chr1-79354088; COSMIC: COSV66060435;