1-78762271-C-T

Variant names:

• chr1-78762271-C-T
• rs1937020

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 0.635 in 152,048 control chromosomes in the GnomAD database, including 31,089 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 0.63 (31089 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 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: 0.635 AC: 96452 AN: 151930 Hom.: 31057 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.635 AC: 96545 AN: 152048 Hom.: 31089 Cov.: 33 AF XY: 0.632 AC XY: 46949 AN XY: 74320

African (AFR) AF: 0.574 AC: 23823 AN: 41470

American (AMR) AF: 0.627 AC: 9572 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2175 AN: 5172

South Asian (SAS) AF: 0.592 AC: 2856 AN: 4824

European-Finnish (FIN) AF: 0.705 AC: 7441 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46672 AN: 67972

Other (OTH) AF: 0.618 AC: 1306 AN: 2112

Alfa AF: 0.660 Hom.: 107376

Bravo AF: 0.626

Asia WGS AF: 0.515 AC: 1794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.58
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1937020; hg19: chr1-79227956;