chr1-115192428-C-T

Position:

• chr1-115192428-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 0.258 in 152,108 control chromosomes in the GnomAD database, including 6,453 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 0.26 (6453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.258 AC: 39287 AN: 151990 Hom.: 6454 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.258 AC: 39270 AN: 152108 Hom.: 6453 Cov.: 32 AF XY: 0.251 AC XY: 18684 AN XY: 74358

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.00310

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.290

Alfa AF: 0.302 Hom.: 1355

Bravo AF: 0.244

Asia WGS AF: 0.0880 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.086
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489532; hg19: chr1-115735049;