1-78589705-C-T

Variant names:

• chr1-78589705-C-T
• rs10518577

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 0.638 in 151,898 control chromosomes in the GnomAD database, including 33,192 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 0.64 (33192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.749 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: 0.639 AC: 96969 AN: 151780 Hom.: 33195 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.638 AC: 96974 AN: 151898 Hom.: 33192 Cov.: 32 AF XY: 0.643 AC XY: 47714 AN XY: 74246

African (AFR) AF: 0.373 AC: 15458 AN: 41462

American (AMR) AF: 0.760 AC: 11571 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2816 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3552 AN: 5136

South Asian (SAS) AF: 0.608 AC: 2929 AN: 4820

European-Finnish (FIN) AF: 0.797 AC: 8435 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49777 AN: 67892

Other (OTH) AF: 0.681 AC: 1439 AN: 2114

Alfa AF: 0.614 Hom.: 4541

Bravo AF: 0.630

Asia WGS AF: 0.612 AC: 2133 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.54
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10518577; hg19: chr1-79055390; COSMIC: COSV70038199;