4-116401752-T-A

Position:

• chr4-116401752-T-A

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 0.125 in 152,170 control chromosomes in the GnomAD database, including 1,235 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 0.12 (1235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

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 (AMR) allele frequency at 95% confidence interval = 0.144 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: 0.125 AC: 18935 AN: 152050 Hom.: 1238 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.125 AC: 18947 AN: 152170 Hom.: 1235 Cov.: 32 AF XY: 0.128 AC XY: 9553 AN XY: 74368

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0485 Hom.: 41

Bravo AF: 0.126

Asia WGS AF: 0.102 AC: 358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6811925; hg19: chr4-117322908;