rs1459544

chr4-117717418-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 0.15 in 152,170 control chromosomes in the GnomAD database, including 2,237 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 0.15 (2237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• 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: 0.150 AC: 22812 AN: 152052 Hom.: 2234 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.150 AC: 22848 AN: 152170 Hom.: 2237 Cov.: 32 AF XY: 0.145 AC XY: 10811 AN XY: 74398

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0565

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.162

Alfa AF: 0.111 Hom.: 491

Bravo AF: 0.163

Asia WGS AF: 0.134 AC: 465 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	11
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459544; hg19: chr4-118638573;