1-181070392-C-T

Position:

• chr1-181070392-C-T

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 0.0426 in 152,326 control chromosomes in the GnomAD database, including 172 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 0.043 (172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0562 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: 0.0426 AC: 6480 AN: 152208 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0426 AC: 6482 AN: 152326 Hom.: 172 Cov.: 32 AF XY: 0.0413 AC XY: 3079 AN XY: 74498

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0479

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0485 Hom.: 217

Bravo AF: 0.0426

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17302632; hg19: chr1-181039528;