1-78798120-T-C

Variant names:

• chr1-78798120-T-C
• rs10873998

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 0.504 in 151,700 control chromosomes in the GnomAD database, including 20,216 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 0.50 (20216 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76419 AN: 151582 Hom.: 20206 Cov.: 29

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.504 AC: 76458 AN: 151700 Hom.: 20216 Cov.: 29 AF XY: 0.512 AC XY: 37912 AN XY: 74080

African (AFR) AF: 0.349 AC: 14448 AN: 41346

American (AMR) AF: 0.578 AC: 8800 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1619 AN: 3462

East Asian (EAS) AF: 0.716 AC: 3665 AN: 5120

South Asian (SAS) AF: 0.571 AC: 2744 AN: 4806

European-Finnish (FIN) AF: 0.595 AC: 6247 AN: 10498

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37397 AN: 67934

Other (OTH) AF: 0.478 AC: 1005 AN: 2104

Alfa AF: 0.533 Hom.: 82954

Bravo AF: 0.498

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.80
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10873998; hg19: chr1-79263805;