1-78888403-C-T

Variant names:

• chr1-78888403-C-T
• rs10518590

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0187 AC: 778 AN: 41508

American (AMR) AF: 0.0424 AC: 648 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5168

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4824

European-Finnish (FIN) AF: 0.0362 AC: 382 AN: 10556

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0536 AC: 3642 AN: 67978

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0103 Hom.: 3

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

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