rs2689178

Variant names:

• chr1-238767053-T-C
• rs2689178

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 0.673 in 152,026 control chromosomes in the GnomAD database, including 35,004 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 0.67 (35004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.673 AC: 102201 AN: 151908 Hom.: 34956 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.673 AC: 102312 AN: 152026 Hom.: 35004 Cov.: 32 AF XY: 0.667 AC XY: 49564 AN XY: 74316

African (AFR) AF: 0.750 AC: 31112 AN: 41488

American (AMR) AF: 0.717 AC: 10945 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1939 AN: 5156

South Asian (SAS) AF: 0.514 AC: 2480 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6585 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44783 AN: 67944

Other (OTH) AF: 0.669 AC: 1413 AN: 2112

Alfa AF: 0.659 Hom.: 15761

Bravo AF: 0.682

Asia WGS AF: 0.457 AC: 1586 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2689178; hg19: chr1-238930353;