1-155154472-T-C

Position:

• chr1-155154472-T-C

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 0.424 in 151,988 control chromosomes in the GnomAD database, including 14,350 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 0.42 (14350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64352 AN: 151870 Hom.: 14344 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.424 AC: 64386 AN: 151988 Hom.: 14350 Cov.: 32 AF XY: 0.430 AC XY: 31949 AN XY: 74274

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.409

Alfa AF: 0.395 Hom.: 1501

Bravo AF: 0.431

Asia WGS AF: 0.595 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908458; hg19: chr1-155126948;