1-154356067-C-T

Variant names:

• chr1-154356067-C-T
• rs10908831

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.345 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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.398

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908831; hg19: chr1-154328543;