4-145983152-C-T

Variant names:

• chr4-145983152-C-T
• rs11100904

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 0.365 in 149,064 control chromosomes in the GnomAD database, including 10,567 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 0.37 (10567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 54448 AN: 148946 Hom.: 10567 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.365 AC: 54478 AN: 149064 Hom.: 10567 Cov.: 32 AF XY: 0.356 AC XY: 25960 AN XY: 72852

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0875

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.317

Alfa AF: 0.398 Hom.: 20804

Bravo AF: 0.356

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11100904; hg19: chr4-146904304;