1-78711183-C-T

Variant names:

• chr1-78711183-C-T
• rs4650376

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 0.844 in 152,084 control chromosomes in the GnomAD database, including 54,193 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 0.84 (54193 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128253 AN: 151966 Hom.: 54163 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.844 AC: 128337 AN: 152084 Hom.: 54193 Cov.: 31 AF XY: 0.846 AC XY: 62867 AN XY: 74332

African (AFR) AF: 0.842 AC: 34913 AN: 41472

American (AMR) AF: 0.871 AC: 13311 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2943 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5029 AN: 5182

South Asian (SAS) AF: 0.881 AC: 4243 AN: 4816

European-Finnish (FIN) AF: 0.844 AC: 8914 AN: 10564

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56330 AN: 67992

Other (OTH) AF: 0.858 AC: 1807 AN: 2106

Alfa AF: 0.839 Hom.: 75123

Bravo AF: 0.847

Asia WGS AF: 0.927 AC: 3212 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4650376; hg19: chr1-79176868;