chr1-113348496-C-T

Position:

• chr1-113348496-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 0.302 in 151,680 control chromosomes in the GnomAD database, including 8,312 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 0.30 (8312 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 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: 0.303 AC: 45865 AN: 151564 Hom.: 8308 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.302 AC: 45868 AN: 151680 Hom.: 8312 Cov.: 31 AF XY: 0.303 AC XY: 22480 AN XY: 74086

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.290

Alfa AF: 0.367 Hom.: 7884

Bravo AF: 0.286

Asia WGS AF: 0.305 AC: 1064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9308261; hg19: chr1-113891118;