chr1-154356067-C-T

Variant names:

• chr1-154356067-C-T
• rs10908831

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 0.344 in 152,142 control chromosomes in the GnomAD database, including 10,640 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 0.34 (10640 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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: 0.345 AC: 52404 AN: 152024 Hom.: 10638 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.344 AC: 52409 AN: 152142 Hom.: 10640 Cov.: 33 AF XY: 0.348 AC XY: 25873 AN XY: 74362

African (AFR) AF: 0.123 AC: 5104 AN: 41534

American (AMR) AF: 0.455 AC: 6949 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3138 AN: 5176

South Asian (SAS) AF: 0.502 AC: 2421 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3820 AN: 10572

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27853 AN: 67966

Other (OTH) AF: 0.398 AC: 840 AN: 2112

Alfa AF: 0.361 Hom.: 1332

Bravo AF: 0.344

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.30
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10908831; hg19: chr1-154328543;