chr4-118387448-T-C

Position:

• chr4-118387448-T-C

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 0.153 in 151,890 control chromosomes in the GnomAD database, including 2,111 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 (2111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

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 (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.153 AC: 23196 AN: 151776 Hom.: 2114 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23196 AN: 151890 Hom.: 2111 Cov.: 31 AF XY: 0.156 AC XY: 11585 AN XY: 74224

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0764

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.152

Alfa AF: 0.180 Hom.: 621

Bravo AF: 0.137

Asia WGS AF: 0.135 AC: 468 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	5.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11722450; hg19: chr4-119308603;