1-78746244-C-T

Position:

• chr1-78746244-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 0.876 in 152,084 control chromosomes in the GnomAD database, including 58,479 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 0.88 (58479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.876 AC: 133188 AN: 151966 Hom.: 58426 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.876 AC: 133298 AN: 152084 Hom.: 58479 Cov.: 32 AF XY: 0.878 AC XY: 65242 AN XY: 74322

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.897

Alfa AF: 0.854 Hom.: 61289

Bravo AF: 0.881

Asia WGS AF: 0.941 AC: 3257 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033999; hg19: chr1-79211929;