1-119435210-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 0.123 in 208,918 control chromosomes in the GnomAD database, including 2,359 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 0.14 (2133 hom., cov: 33)
  • Exomes 𝑓: 0.077 (226 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21297 AN: 152050 Hom.: 2129 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.0771 AC: 4373 AN: 56750 Hom.: 226 AF XY: 0.0781 AC XY: 2323 AN XY: 29732

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.122

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.0558

Gnomad4 SAS exome AF: 0.0986

Gnomad4 FIN exome AF: 0.0346

Gnomad4 NFE exome AF: 0.0685

Gnomad4 OTH exome AF: 0.0736

GnomAD4 genome AF: 0.140 AC: 21327 AN: 152168 Hom.: 2133 Cov.: 33 AF XY: 0.139 AC XY: 10337 AN XY: 74410

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0518 Hom.: 91

Bravo AF: 0.155

Asia WGS AF: 0.106 AC: 372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417608; hg19: chr1-119977833;