1-78746244-C-T

Variant names:

• chr1-78746244-C-T
• rs1033999

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 0.876 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.910 AC: 37789 AN: 41514

American (AMR) AF: 0.880 AC: 13417 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3125 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5094 AN: 5178

South Asian (SAS) AF: 0.913 AC: 4395 AN: 4816

European-Finnish (FIN) AF: 0.870 AC: 9220 AN: 10594

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57484 AN: 67936

Other (OTH) AF: 0.897 AC: 1899 AN: 2116

Alfa AF: 0.857 Hom.: 76980

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1033999; hg19: chr1-79211929;