chr4-116954105-T-G

Position:

• chr4-116954105-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.223 in 151,898 control chromosomes in the GnomAD database, including 3,870 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 0.22 (3870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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: 0.223 AC: 33843 AN: 151778 Hom.: 3868 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.223 AC: 33861 AN: 151898 Hom.: 3870 Cov.: 32 AF XY: 0.223 AC XY: 16525 AN XY: 74238

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.261

Alfa AF: 0.206 Hom.: 1836

Bravo AF: 0.226

Asia WGS AF: 0.270 AC: 939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440306; hg19: chr4-117875261;